Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:6.2.1.1 (ACS)
78,556 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The findings presented here originally arose from the suggestion that the synthesis of dinucleoside polyphosphates (Np(n)N) may be a general process involving enzyme ligases catalyzing the transfer of a nucleotidyl moiety via nucleotidyl-containing intermediates, with release of pyrophosphate. Within this context, the characteristics of the following enzymes are presented. Firefly luciferase (EC 1.12. 13.7), an oxidoreductase with characteristics of a ligase, synthesizes a variety of (di)nucleoside polyphosphates with four or more inner phosphates. The discrepancy between the kinetics of light production and that of Np(n)N synthesis led to the finding that E*L-AMP (L = dehydroluciferin), formed from the E*LH(2)-AMP complex (LH(2) = luciferin) shortly after the onset of the reaction, was the main intermediate in the synthesis of (di)nucleoside polyphosphates. Acetyl-CoA synthetase (EC 6.2.1.1) and acyl-CoA synthetase (EC 6.2.1. 8) are ligases that synthesize p(4)A from ATP and P(3) and, to a lesser extent, Np(n)N. T4 DNA ligase (EC 6.5.1.1) and T4 RNA ligase (EC 6.5.1.3) catalyze the synthesis of Np(n)N through the formation of an E-AMP complex with liberation of pyrophosphate. DNA is an inhibitor of the synthesis of Np(n)N and conversely, P(3) or nucleoside triphosphates inhibit the ligation of a single-strand break in duplex DNA catalyzed by T4 DNA ligase, which could have therapeutic implications. The synthesis of Np(n)N catalyzed by T4 RNA ligase is inhibited by nucleoside 3'(2'),5'-bisphosphates. Reverse transcriptase (EC 2.7.7.49), although not a ligase, catalyzes, as reported by others, the synthesis of Np(n)ddN in the process of removing a chain termination residue at the 3'-OH end of a growing DNA chain.
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PMID:Synthesis of dinucleoside polyphosphates catalyzed by firefly luciferase and several ligases. 1100 93

The present study evaluates the expression of genes of Giardia lamblia, one of the most simple and most early diverging eukaryotes, that encode the metabolic enzymes pyruvate: ferredoxin oxidoreductase (PFOR), acetyl-CoA synthetase (ACS), alcohol dehydrogenase E (ADHE) and glutamate dehydrogenase (GDH) and the cyst wall protein (CWP1) gene in trophozoites, cysts and during the excystation process. Primers were designed to amplify mRNA fragments through quantitative reverse-transcriptase-polymerase-chain-reaction. In trophozoites, all transcripts of the enzymes studied were present. In cysts, three of the transcripts were detected: CWP1, GDH and ACS; but the relative levels of the mRNA of GDH and ACS were very different between trophozoites and cysts. During excystation, PFOR and ADHE transcripts appeared after the first induction phase, and the mRNAs of ACS and GDH increased throughout the process.
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PMID:Transcription of metabolic enzyme genes during the excystation of Giardia lamblia. 1466 85

The objective of this prospective study was to investigate if Chlamydophila pneumoniae (Cp)-specific DNA and mRNA are present in tissue samples from the wall of aorta ascendens in patients undergoing by-pass surgery for coronary artery disease (CAD) that includes stable angina pectoris (SAP, 25 patients) and acute coronary syndrome (ACS, 19 patients). Viable Cp was detected in 8/44 (18%) patients using reversed transcriptase PCR (RT-PCR) against bacterial mRNA with detection of cDNA using real-time PCR against the MOMP gene. Cp DNA was detected by nested PCR in 22/44 (50%) patients and by real-time PCR in 13/44 (30%) patients. In total, 24/44 (55%) patients were positive for Cp nucleic acid in any PCR. Antibodies to Cp were detected in 13/24 (54%) Cp PCR-positive and in 15/20 (75%) Cp PCR-negative patients. Nested PCR was run on throat swabs from all patients. No significant differences were noted between SAP and ACS patients regarding PCR results or serology. It has been suggested that Cp may be a 'silent passenger' picked up by the atherosclerotic plaque. Our findings of viable and metabolically active bacteria in aortic tissue add further support to the hypothesis that Cp may have an active role in the pathogenesis of atherosclerosis.
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PMID:Chlamydophila pneumonia: Specific mRNA in aorta ascendens in patients undergoing coronary artery by-pass grafting. 1693 28

Gold nanorods (GNRs) stabilized with cetyltrimethylammonium bromide (CTAB) and GNR functionalized via a ligand exchange method with either thiolated polyethylene glycol (PEG(5000)) or mercaptohexadecanoic acid (MHDA) were investigated for their stability in biological media and subsequent toxicological effects to HaCaT cells. GNR-PEG and GNR-MHDA exhibited minimal effects on cell proliferation, whereas GNR-CTAB reduced cell proliferation significantly due to the inherent toxicity of the cationic surfactant to cells. Cell uptake studies indicated relatively low uptake for GNR-PEG and high uptake for GNR-MHDA. Reverse transcriptase polymerase chain reaction (RT-PCR) revealed that GNR-PEG induced less significant and unique changes in the transcription levels of 84 genes related to stress and toxicity compared to GNR-MHDA. The results demonstrate that, although cell proliferation was not affected by both particles, there is a significant difference in gene expression in GNR-MHDA exposed cells, suggesting long-term implications for chronic exposure.
ACS Nano 2011 Apr 26
PMID:Effect of gold nanorod surface chemistry on cellular response. 2140 2

Osteointegration of titanium implants in bone defects is clinically important for long-term performance of orthopaedic implants. In this work, we developed a facile and effective "one-pot" deposition method based on dopamine polymerization for the development of cell-adhesive, osteoconductive, and osteoinductive titanium implants. Arg-Gly-Asp (RGD)-conjugated polymers, hydroxyapatite (HAp) nanoparticles, and bone morphogenic protein-2 (BMP-2) were mixed with an alkaline dopamine solution, and then, titanium substrates were immersed in the mixture for an hour. During poly(dopamine) coating, the three types of bioactive substances were immobilized on the titanium surfaces. Our results indicate that RGD conjugation enhanced the adhesion of human bone marrow stem cell line, while HAp incorporation facilitated cellular osteodifferentiation. The immobilization of BMP-2 induced the osteogenesis of the stem cells, indicated by reverse-transcriptase polymerase chain reaction (RT-PCR) analysis. The mineralization on the deposited substrates was also enhanced greatly. This functionalized layer on titanium substrate promoted mesenchymal stem cell to osteoblast and improved osteogenic differentiation and mineralization. In conclusion, the surface modification method shows a great potential for enhancement of osteointegration of orthopaedic and dental implants.
ACS Appl Mater Interfaces 2013 Aug 14
PMID:Poly(dopamine)-assisted immobilization of Arg-Gly-Asp peptides, hydroxyapatite, and bone morphogenic protein-2 on titanium to improve the osteogenesis of bone marrow stem cells. 2384 58

The influenza virus RNA-dependent RNA polymerase complex (RdRp), a heterotrimeric protein complex responsible for viral RNA transcription and replication, represents a primary target for antiviral drug development. One particularly attractive approach is interference with the endonucleolytic "cap-snatching" reaction by the RdRp subunit PA, more precisely by inhibiting its metal-dependent catalytic activity which resides in the N-terminal part of PA (PA-Nter). Almost all PA inhibitors (PAIs) thus far discovered bear pharmacophoric fragments with chelating motifs able to bind the bivalent metal ions in the catalytic core of PA-Nter. More recently, the availability of crystallographic structures of PA-Nter has enabled rational design of original PAIs with improved binding properties and antiviral potency. We here present a coupled pharmacophore/docking virtual screening approach that allowed us to identify PAIs with interesting inhibitory activity in a PA-Nter enzymatic assay. Moreover, antiviral activity in the low micromolar range was observed in cell-based influenza virus assays.
ACS Med Chem Lett 2015 Aug 13
PMID:Virtual Screening and Biological Validation of Novel Influenza Virus PA Endonuclease Inhibitors. 2628 86

Domain II of the nonstructural protein 5 (NS5A) of the hepatitis C virus (HCV) is involved in intermolecular interactions with the viral RNA genome, the RNA-dependent RNA polymerase NS5B, and the host factor cyclophilin A (CypA). However, domain II of NS5A (NS5A^DII) is largely disordered, which makes it difficult to characterize the protein-protein or protein-nucleic acid interfaces. Here we utilized a mass spectrometry-based protein footprinting approach in attempts to characterize regions forming contacts between NS5A^DII and its binding partners. In particular, we compared surface topologies of lysine and arginine residues in the context of free and bound NS5A^DII. These experiments have led to the identification of an RNA binding motif (³⁰⁵RSRKFPR³¹¹) in an arginine-rich region of NS5A^DII. Furthermore, we show that K308 is indispensable for both RNA and NS5B binding, whereas W316, further downstream, is essential for protein-protein interactions with CypA and NS5B. Most importantly, NS5A^DII binding to NS5B involves a region associated with RNA binding within NS5B. This interaction down-regulated RNA synthesis by NS5B, suggesting that NS5A^DII modulates the activity of NS5B and potentially regulates HCV replication.
ACS Infect Dis 2016 11 11
PMID:Interactions of the Disordered Domain II of Hepatitis C Virus NS5A with Cyclophilin A, NS5B, and Viral RNA Show Extensive Overlap. 2767 32

Small synthetic fluorophores are in many ways superior to fluorescent proteins as labels for imaging. A major challenge is to use them for a protein-specific labeling in living cells. Here, we report on our use of noncanonical amino acids that are genetically encoded via the pyrrolysyl-tRNA/pyrrolysyl-RNA synthetase pair at artificially introduced TAG codons in a recoded E. coli strain. The strain is lacking endogenous TAG codons and the TAG-specific release factor RF1. The amino acids contain bioorthogonal groups that can be clicked to externally supplied dyes, thus enabling protein-specific labeling in live cells. We find that the noncanonical amino acid incorporation into the target protein is robust for diverse amino acids and that the usefulness of the recoded E. coli strain mainly derives from the absence of release factor RF1. However, the membrane permeable dyes display high nonspecific binding in intracellular environment and the electroporation of hydrophilic nonmembrane permeable dyes severely impairs growth of the recoded strain. In contrast, proteins exposed on the outer membrane of E. coli can be labeled with hydrophilic dyes with a high specificity as demonstrated by labeling of the osmoporin OmpC. Here, labeling can be made sufficiently specific to enable single molecule studies as exemplified by OmpC single particle tracking.
ACS Synth Biol 2017 02 17
PMID:Application of Noncanonical Amino Acids for Protein Labeling in a Genomically Recoded Escherichia coli. 2777 82

We investigated the osteogenic potential of nitrogen-doped carbon dots (NCDs) conjugated with hydroxyapatite (HA) nanoparticles on the MC3T3-E1 osteoblast cell functions and in a zebrafish (ZF) jawbone regeneration (JBR) model. The NCDs-HA nanoparticles were fabricated by a hydrothermal cum co-precipitation technique. The surface structures of NCDs-HA nanoparticles were characterized by X-ray diffraction; Fourier transform infrared (FTIR), UV-vis, and laser fluorescence spectroscopies; and scanning electron microscopy, transmission electron microscopy (TEM), energy-dispersive spectrometry (EDS), and NMR analyses. The TEM data confirmed that the NCDs are well conjugated on the HA nanoparticle surfaces. The fluorescent spectroscopy results indicated that the NCDs-HA exhibited promising luminescent emission in vitro. Finally, we validated the chemical structure of NCDs-HA nanoparticles on the basis of FTIR, EDS, and ³¹P NMR analysis and observed that NCDs are bound with HA by electrostatic interaction and H-bonding. Cell proliferation assay, alkaline phosphatase, and Alizarin red staining were used to confirm the effect of NCDs-HA nanoparticles on MC3T3-E1 osteoblast proliferation, differentiation, and mineralization, respectively. Reverse transcriptase polymerase chain reaction was used to measure the expression of the osteogenic genes like runt-related transcription factor 2, alkaline phosphatase, and osteocalcin. ZF-JBR model was used to confirm the effect of NCDs-HA nanoparticles on bone regeneration. NCDs-HA nanoparticles demonstrated cell imaging ability, enhanced alkaline phosphatase activity, mineralization, and expression of the osteogenic genes in osteoblast cells, indicating possible theranostic function. Further, NCDs-HA nanoparticles significantly enhanced ZF bone regeneration and mineral density compared to HA nanoparticles, indicating a therapeutic potential of NCDs-HA nanoparticles in bone regeneration and fracture healing.
ACS Appl Mater Interfaces 2018 Jun 13
PMID:Accelerated Bone Regeneration by Nitrogen-Doped Carbon Dots Functionalized with Hydroxyapatite Nanoparticles. 2978 48

An RNA-dependent RNA polymerase ribozyme that was highly optimized through in vitro evolution for the ability to copy a broad range of template sequences exhibits promiscuity toward other nucleic acids and nucleic acid analogues, including DNA, threose nucleic acid (TNA), and arabinose nucleic acid (ANA). By operating on various RNA templates, the ribozyme catalyzes multiple successive additions of DNA, TNA, or ANA monomers, although with reduced efficiency compared to RNA monomers. The ribozyme can also copy DNA or TNA templates to complementary RNAs, and to a lesser extent it can operate when both the template and product strands are composed of DNA, TNA, or ANA. These results suggest that polymerase ribozymes, which are thought to have replicated RNA genomes during the early history of life, could have transferred RNA-based genetic information to and from DNA, enabling the emergence of DNA genomes prior to the emergence of proteins. In addition, genetic systems based on nucleic acid-like molecules, which have been proposed as precursors or contemporaries of RNA-based life, could have been operated upon by a promiscuous polymerase ribozyme, thus enabling the evolutionary transition between early genetic systems.
ACS Synth Biol 2019 05 17
PMID:RNA-Catalyzed Polymerization of Deoxyribose, Threose, and Arabinose Nucleic Acids. 3104 60


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