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The Journal of Physical Chemistry. B Dec 2022Autofluorescence imaging has been widely applied as advanced noninvasive diagnostics for in vivo and ex vivo tissues. The optical redox ratio (ORR), which is defined as...
Autofluorescence imaging has been widely applied as advanced noninvasive diagnostics for in vivo and ex vivo tissues. The optical redox ratio (ORR), which is defined as the fluorescence intensity ratio between reduced nicotine adenine dinucleotide (NADH) and oxidized flavin adenine dinucleotide (FAD), has been used as a diagnostic parameter strongly, because NADH and FAD play an important role in energetic and respiratory metabolism as coenzymes. The ORR method has provided successful assessment in cancer diagnosis including breast, cervical, and oral cancer; few studies have been reported about optical and chemical interference between two molecules resulting in a change in ORR values. In this study, we investigated the variations in ORR values of NADH/FAD mixtures dissolved in tris(hydroxymethyl)aminomethane, phosphate buffer, and deionized water environments. In vitro solutions were prepared in various concentration ratios and the experimental and theoretical ORR values were obtained from fluorescence and absorption spectra in time series. Based on the spectroscopic analysis, we concluded that the inner filter effect causes an instant decrease in FAD fluorescence just after dissolution and that the oxidation-reduction coupled with oxygenation reaction results in time-varying decreases in NADH fluorescence and FAD emission.
Topics: Adenine; Nicotine; Flavin-Adenine Dinucleotide; NAD; Dinucleoside Phosphates; Oxidation-Reduction
PubMed: 36399328
DOI: 10.1021/acs.jpcb.2c05292 -
Communications Biology Jul 2022Predicting protein-protein interaction and non-interaction are two important different aspects of multi-body structure predictions, which provide vital information about...
Predicting protein-protein interaction and non-interaction are two important different aspects of multi-body structure predictions, which provide vital information about protein function. Some computational methods have recently been developed to complement experimental methods, but still cannot effectively detect real non-interacting protein pairs. We proposed a gene sequence-based method, named NVDT (Natural Vector combine with Dinucleotide and Triplet nucleotide), for the prediction of interaction and non-interaction. For protein-protein non-interactions (PPNIs), the proposed method obtained accuracies of 86.23% for Homo sapiens and 85.34% for Mus musculus, and it performed well on three types of non-interaction networks. For protein-protein interactions (PPIs), we obtained accuracies of 99.20, 94.94, 98.56, 95.41, and 94.83% for Saccharomyces cerevisiae, Drosophila melanogaster, Helicobacter pylori, Homo sapiens, and Mus musculus, respectively. Furthermore, NVDT outperformed established sequence-based methods and demonstrated high prediction results for cross-species interactions. NVDT is expected to be an effective approach for predicting PPIs and PPNIs.
Topics: Animals; Dinucleoside Phosphates; Drosophila melanogaster; Genetic Techniques; Genetic Vectors; Helicobacter pylori; Mice; Saccharomyces cerevisiae
PubMed: 35780196
DOI: 10.1038/s42003-022-03617-0 -
Chemistry (Weinheim An Der Bergstrasse,... May 2024Biomolecules containing adenosine di- or triphosphate (ADP or ATP) are crucial for diverse biological processes. Synthesis of these biomolecules and development of their...
Biomolecules containing adenosine di- or triphosphate (ADP or ATP) are crucial for diverse biological processes. Synthesis of these biomolecules and development of their chemical probes are important to elucidate their functions. Enabling reproducible and high-yielding access to these ADP- and ATP-containing molecules via conventional P(III)-P(V) and P(V)-P(V) coupling reactions is challenging owing to water content in highly polar phosphate-containing substrates. Herein, we report an efficient and reliable method for protecting-group-free P(V)-P(V) coupling reaction through in situ activation of phosphates using hydrolysis-stable 2-[N-(2-methylimidazoyl)]-1,3-dimethylimidazolinium chloride (2-MeImIm-Cl), providing the corresponding electrophilic P(V) intermediates for subsequent nucleophilic attack using their coupling partners. This P(V)-P(V) coupling reaction proceeded even in a wet reaction medium and showed a broad substrate scope, accommodating protecting-group-free synthesis of ADP-ribose and nicotinamide adenine diphosphate analogs, ATP-containing biomolecules, and ADP-ribosyl peptides.
PubMed: 38763895
DOI: 10.1002/chem.202401302 -
Current Opinion in Microbiology Apr 2016Bacteria that synthesize c-di-AMP also encode several mechanisms for controlling c-di-AMP levels within the cytoplasm. One major class of phosphodiesterases comprises... (Review)
Review
Bacteria that synthesize c-di-AMP also encode several mechanisms for controlling c-di-AMP levels within the cytoplasm. One major class of phosphodiesterases comprises GdpP and DhhP homologs, which degrade c-di-AMP into the linear molecule 5'-pApA or AMP by the DHH-DHHA1 domain. The other major class comprises PgpH homologs, which degrade c-di-AMP by the HD domain. Both GdpP and PgpH harbor sensory domains, likely to regulate c-di-AMP hydrolysis activity in response to signal input. As another possible mechanism for controlling cytoplasmic c-di-AMP levels, bacteria also secrete c-di-AMP via multidrug resistance transporters, as demonstrated for Listeria monocytogenes. Mutants that accumulate high c-di-AMP levels, by deletion of phosphodiesterases or multidrug resistance transporters, exhibit aberrant physiology, growth defects, and attenuated virulence in infection.
Topics: Bacteria; Bacterial Proteins; Cytoplasm; Dinucleoside Phosphates; Gene Expression Regulation, Bacterial; Phosphoric Diester Hydrolases
PubMed: 26773214
DOI: 10.1016/j.mib.2015.12.007 -
Nature Communications Feb 2020It has been more than 50 years since the discovery of dinucleoside polyphosphates (NpNs) and yet their roles and mechanisms of action remain unclear. Here, we show that...
It has been more than 50 years since the discovery of dinucleoside polyphosphates (NpNs) and yet their roles and mechanisms of action remain unclear. Here, we show that both methylated and non-methylated NpNs serve as RNA caps in Escherichia coli. NpNs are excellent substrates for T7 and E. coli RNA polymerases (RNAPs) and efficiently initiate transcription. We demonstrate, that the E. coli enzymes RNA 5'-pyrophosphohydrolase (RppH) and bis(5'-nucleosyl)-tetraphosphatase (ApaH) are able to remove the NpN-caps from RNA. ApaH is able to cleave all NpN-caps, while RppH is unable to cleave the methylated forms suggesting that the methylation adds an additional layer to RNA stability regulation. Our work introduces a different perspective on the chemical structure of RNA in prokaryotes and on the role of RNA caps. We bring evidence that small molecules, such as NpNs are incorporated into RNA and may thus influence the cellular metabolism and RNA turnover.
Topics: Acid Anhydride Hydrolases; DNA-Directed RNA Polymerases; Dinucleoside Phosphates; Escherichia coli; Escherichia coli Proteins; Methylation; Nucleic Acid Conformation; RNA Caps; RNA Stability; RNA, Bacterial
PubMed: 32103016
DOI: 10.1038/s41467-020-14896-8 -
International Urogynecology Journal Oct 2021This systematic review evaluated the rigor of the development of clinical practice guidelines (CPG). (Review)
Review
INTRODUCTION AND HYPOTHESIS
This systematic review evaluated the rigor of the development of clinical practice guidelines (CPG).
METHODS
The searched sources were MEDLINE, EMBASE, Web of Science, Scopus, and specific databases of CPG. Reviewers, organized in triplicate and independently, selected the studies and assessed the quality of the guidelines using the Appraisal of Guidelines Research and Evaluation (AGREE II) instrument, which contains six domains for classification. The classification of the CPGs prioritized the domain 3 (developmental rigor) considering: high (score > 60%), moderate (score 30-60%), or low quality (score < 30%). The results were checked for discrepancies and decided by consensus. The interventions were described. Descriptive statistics presented the results.
RESULTS
Of the ten CPGs evaluated, five were of high methodological quality, three were of moderate quality, and two of low quality. Three documents were not recommended for use. The domains with the highest scores were scope and purpose (mean = 90.1%) and clarity of presentation (mean = 88.9%). The domains of editorial independence (mean = 41.4%) and applicability (mean = 29.3%) were those with the lowest score. The most cited interventions in CPGs were the nonpharmacological, such as lifestyle interventions, bladder training, or re-education and pelvic floor muscle training.
CONCLUSION
Most guidelines showed rigor in development and were recommended for use; however, editorial independence and applicability were domains that need to be improved in these documents. Our findings can guide the choice of CPG for the treatment of urinary incontinence.
Topics: Bibliometrics; Databases, Factual; Dinucleoside Phosphates; Humans; Life Style; Urinary Incontinence
PubMed: 33704538
DOI: 10.1007/s00192-021-04729-7 -
Nature Communications Jan 2022Mammalian innate immune sensor STING (STimulator of INterferon Gene) was recently found to originate from bacteria. During phage infection, bacterial STING sense...
Mammalian innate immune sensor STING (STimulator of INterferon Gene) was recently found to originate from bacteria. During phage infection, bacterial STING sense c-di-GMP generated by the CD-NTase (cGAS/DncV-like nucleotidyltransferase) encoded in the same operon and signal suicide commitment as a defense strategy that restricts phage propagation. However, the precise binding mode of c-di-GMP to bacterial STING and the specific recognition mechanism are still elusive. Here, we determine two complex crystal structures of bacterial STING/c-di-GMP, which provide a clear picture of how c-di-GMP is distinguished from other cyclic dinucleotides. The protein-protein interactions further reveal the driving force behind filament formation of bacterial STING. Finally, we group the bacterial STING into two classes based on the conserved motif in β-strand lid, which dictate their ligand specificity and oligomerization mechanism, and propose an evolution-based model that describes the transition from c-di-GMP-dependent signaling in bacteria to 2'3'-cGAMP-dependent signaling in eukaryotes.
Topics: Bacteria; Crystallography, X-Ray; Cyclic GMP; Dinucleoside Phosphates; Humans; Immunity, Innate; Interferons; Ligands; Membrane Proteins; Nucleotidyltransferases; Prevotella
PubMed: 35013136
DOI: 10.1038/s41467-021-26583-3 -
Journal of Ocular Pharmacology and... 2017Diadenosine tetraphosphate abbreviated ApA is a naturally occurring dinucleotide, which is present in most of the ocular fluids. Due to its intrinsic resistance to... (Review)
Review
Diadenosine tetraphosphate abbreviated ApA is a naturally occurring dinucleotide, which is present in most of the ocular fluids. Due to its intrinsic resistance to enzyme degradation compared to mononucleotides, this molecule can exhibit profound actions on ocular tissues, including the ocular surface, ciliary body, trabecular meshwork, and probably the retina. The actions of ApA are mostly carried out by P2Y receptors, but the participation of P2X2 and P2Y in processes such as the regulation of intraocular pressure (IOP), together with the P2Y, is pivotal. Beyond the physiological role, this dinucleotide can present on the ocular surface keeping a right production of tear secretion or regulating IOP. It is important to note that exogenous application of ApA to cells or animal models can significantly modify pathophysiological conditions and thus is an attractive therapeutic molecule. The ocular location where ApA actions have not been fully elucidated is in the retina. Although some analogues show interesting actions on pathological situations such as retinal detachment, little is known about the real effect of this dinucleotide, this being one of the challenges that require pursuing in the near future.
Topics: Animals; Dinucleoside Phosphates; Eye; Humans
PubMed: 28414592
DOI: 10.1089/jop.2016.0146 -
Journal of Bacteriology Apr 2023Cyclic dimeric AMP (c-di-AMP) is a widespread second messenger that controls such key functions as osmotic homeostasis, peptidoglycan biosynthesis, and response to... (Review)
Review
Cyclic dimeric AMP (c-di-AMP) is a widespread second messenger that controls such key functions as osmotic homeostasis, peptidoglycan biosynthesis, and response to various stresses. C-di-AMP is synthesized by diadenylate cyclases that contain the DAC (DisA_N) domain, which was originally characterized as the N-terminal domain in the DNA integrity scanning protein DisA. In other experimentally studied diadenylate cyclases, DAC domain is typically located at the protein C termini and its enzymatic activity is controlled by one or more N-terminal domains. As in other bacterial signal transduction proteins, these N-terminal modules appear to sense environmental or intracellular signals through ligand binding and/or protein-protein interactions. Studies of bacterial and archaeal diadenylate cyclases also revealed numerous sequences with uncharacterized N-terminal regions. This work provides a comprehensive review of the N-terminal domains of bacterial and archaeal diadenylate cyclases, including the description of five previously undefined domains and three PK_C-related domains of the DacZ_N superfamily. These data are used to classify diadenylate cyclases into 22 families, based on their conserved domain architectures and the phylogeny of their DAC domains. Although the nature of the regulatory signals remains obscure, the association of certain genes with anti-phage defense CBASS systems and other phage-resistance genes suggests that c-di-AMP might also be involved in the signaling of phage infection.
Topics: Humans; Archaea; Phosphorus-Oxygen Lyases; Bacterial Proteins; Bacteria; Second Messenger Systems; Cyclic AMP; Dinucleoside Phosphates
PubMed: 37022175
DOI: 10.1128/jb.00023-23 -
Nature Mar 2019Cyclic dinucleotides (CDNs) have central roles in bacterial homeostasis and virulence by acting as nucleotide second messengers. Bacterial CDNs also elicit immune...
Cyclic dinucleotides (CDNs) have central roles in bacterial homeostasis and virulence by acting as nucleotide second messengers. Bacterial CDNs also elicit immune responses during infection when they are detected by pattern-recognition receptors in animal cells. Here we perform a systematic biochemical screen for bacterial signalling nucleotides and discover a large family of cGAS/DncV-like nucleotidyltransferases (CD-NTases) that use both purine and pyrimidine nucleotides to synthesize a diverse range of CDNs. A series of crystal structures establish CD-NTases as a structurally conserved family and reveal key contacts in the enzyme active-site lid that direct purine or pyrimidine selection. CD-NTase products are not restricted to CDNs and also include an unexpected class of cyclic trinucleotide compounds. Biochemical and cellular analyses of CD-NTase signalling nucleotides demonstrate that these cyclic di- and trinucleotides activate distinct host receptors and thus may modulate the interaction of both pathogens and commensal microbiota with their animal and plant hosts.
Topics: Animals; Bacterial Proteins; Crystallography, X-Ray; Dinucleoside Phosphates; HEK293 Cells; Humans; Mice; Nucleotides; Nucleotidyltransferases; Operon; Symbiosis
PubMed: 30787435
DOI: 10.1038/s41586-019-0953-5