A structural basis for the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA.

The aminoglycoside resistance conferred by an N1-methylation of A1408 in 16S rRNA by a novel plasmid-mediated methyltransferase NpmA can be a future health threat. In the present study, we have determined crystal structures of the bacterial ribosomal decoding A site with an A1408m1A antibiotic-resistance mutation both in the presence and absence of aminoglycosides. G418 and paromomycin both possessing a 6'-OH group specifically bind to the mutant A site and disturb its function as a molecular switch in the decoding process. On the other hand, binding of gentamicin with a 6'-NH3+ group to the mutant A site could not be observed in the present crystal structure. These observations agree with the minimum inhibitory concentration of aminoglycosides against Escherichia coli. In addition, one of our crystal structures suggests a possible conformational change of A1408 during the N1-methylation reaction by NpmA. The structural information obtained explains how bacteria acquire resistance against aminoglycosides along with a minimum of fitness cost by the N1-methylation of A1408 and provides novel information for designing the next-generation aminoglycoside.

Crystal structure of a NIR-Emitting DNA-Stabilized Ag16 Nanocluster.

DNA has been used as a scaffold to stabilize small, atomically monodisperse silver nanoclusters, which have attracted attention due to their intriguing photophysical properties. Herein, we describe the X-ray crystal structure of a DNA-encapsulated, near-infrared emitting Ag16 nanocluster (DNA-Ag16 NC). The asymmetric unit of the crystal contains two DNA-Ag16 NCs and the crystal packing between the DNA-Ag16 NCs is promoted by several interactions, such as two silver-mediated base pairs between 3'-terminal adenines, two phosphate-Ca2+ -phosphate interactions, and π-stacking between two neighboring thymines. Each Ag16 NC is confined by two DNA decamers that take on a horse-shoe-like conformation and is almost fully shielded from the solvent environment. This structural insight will aid in the determination of the structure/photophysical property relationship for this class of emitters and opens up new research opportunities in fluorescence imaging and sensing using noble-metal clusters.

A Novel DNA Helical Wire Containing HgII -Mediated T:T and T:G Pairs.

Numerous applications of metal-mediated base pairs (metallo-base-pairs) to nucleic acid based nanodevices and genetic code expansion have been extensively studied. Many of these metallo-base-pairs are formed in DNA and RNA duplexes containing Watson-Crick base pairs. Recently, a crystal structure of a metal-DNA nanowire with an uninterrupted one-dimensional silver array was reported. We now report the crystal structure of a novel DNA helical wire containing HgII -mediated T:T and T:G base pairs and water-mediated C:C base pairs. The Hg-DNA wire does not contain any Watson-Crick base pairs. Crystals of the Hg-DNA wire, which is the first DNA wire structure driven by HgII ions, were obtained by mixing the short oligonucleotide d(TTTGC) and HgII ions. This study demonstrates the potential of metallo-DNA to form various structural components that can be used for functional nanodevices.

Canstatin inhibits isoproterenol-induced apoptosis through preserving mitochondrial morphology in differentiated H9c2 cardiomyoblasts.

Canstatin, a non-collagenous fragment, is cleaved from type IV collagen α2 chain, an essential component of basement membrane surrounding cardiomyocytes. Although canstatin is known as an endogenous anti-angiogenic factor, its effects on cardiomyocytes have not been clarified. This study examined the effects of canstatin on isoproterenol-induced apoptosis in differentiated H9c2 cardiomyoblasts. Retinoic acid was used to differentiate H9c2 myoblast to cardiomyocyte-like phenotype. Cell viability was determined by a cell counting assay. Western blotting was performed to detect expression of cleaved casepase-3 and phosphorylation of dynamin related protein (Drp)1 at Ser637 which regulates mitochondrial fission. Mito Sox Red staining was performed to examine a mitochondria-dependent production of reactive oxygen species (ROS). Mitochondrial morphology was detected by Mito Tracker Red staining. Isoproterenol (100 µM, 48 h) significantly decreased cell viability and increased cleaved caspase-3 expression, which were inhibited by canstatin (10-250 ng/ml) in a concentration-dependent manner. Canstatin suppressed the isoproterenol-induced mitochondrial fission but not ROS. Canstatin also inhibited the isoproterenol-induced dephosphorylation of Drp1 at Ser637. In conclusion, canstatin inhibits isoproterenol-induced apoptosis through the inhibition of mitochondrial fission via the suppression of dephosphorylation of Drp1 at Ser637 in differentiated H9c2 cardiomyoblasts.

Direct Intraesophageal Growth from Metastatic Mediastinal Lymphadenopathy in Thymic Carcinoma.

We herein report a case of thymic carcinoma that initially exhibited dysphagia and an intraesophageal mass lesion. A 68-year-old man was admitted to our hospital because of dysphagia. An endoscopic examination revealed a mass on the middle esophagus. Chest computed tomography (CT) showed a huge anterior mediastinal mass and subcarinal lymph node swelling, directly invading into the esophageal lumen. An immunohistological examination of the esophageal and anterior mediastinal masses revealed squamous cell carcinoma originating from the thymus. This is the first report of a thymic carcinoma spreading into the esophageal lumen and forming a mass lesion.

Acute necrotizing encephalopathy and a carnitine palmitoyltransferase 2 variant in an adult.

A 54-year-old Japanese man had a fever of over 40 °C for 7 days and developed unconsciousness, seizure and respiratory arrest. T2-weighted imaging magnetic resonance imaging revealed high-intensity signals on bilateral thalamus and it gradually extended to the brain white matter. Moreover, the lesion progressed to the spinal gray matter. The patient was diagnosed with acute necrotizing encephalopathy. CPT2 variants have been reported to be associated with acute necrotizing encephalopathy particularly in children and spinal cord lesions are extremely rare. We report a case of ANE in an adult with a CPT2 variant who developed spinal cord lesions.

Structure-Based Design of a Eukaryote-Selective Antiprotozoal Fluorinated Aminoglycoside.

Aminoglycosides (AG) are antibiotics that lower the accuracy of protein synthesis by targeting a highly conserved RNA helix of the ribosomal A-site. The discovery of AGs that selectively target the eukaryotic ribosome, but lack activity in prokaryotes, are promising as antiprotozoals for the treatment of neglected tropical diseases, and as therapies to read-through point-mutation genetic diseases. However, a single nucleobase change A1408G in the eukaryotic A-site leads to negligible affinity for most AGs. Herein we report the synthesis of 6'-fluorosisomicin, the first 6'-fluorinated aminoglycoside, which specifically interacts with the protozoal cytoplasmic rRNA A-site, but not the bacterial A-site, as evidenced by X-ray co-crystal structures. The respective dispositions of 6'-fluorosisomicin within the bacterial and protozoal A-sites reveal that the fluorine atom acts only as a hydrogen-bond acceptor to favorably interact with G1408 of the protozoal A-site. Unlike aminoglycosides containing a 6'-ammonium group, 6'-fluorosisomicin cannot participate in the hydrogen-bonding pattern that characterizes stable pseudo-base-pairs with A1408 of the bacterial A-sites. Based on these structural observations it may be possible to shift the biological activity of aminoglycosides to act preferentially as antiprotozoal agents. These findings expand the repertoire of small molecules targeting the eukaryotic ribosome and demonstrate the usefulness of fluorine as a design element.

Crystal structure of a novel RNA motif that allows for precise positioning of a single metal ion.

We have determined a crystal structure of an RNA duplex containing a novel metal-binding motif. The motif is composed of two sheared G○A base pairs, two unpaired A residues and four phosphate groups in close proximity. Four A residues make an A-A-A-A stacking column at the minor groove side and two G bases are highly inclined, thereby forming the pocket-shaped motif at the major groove side. In the present structure, a hydrated Sr2+ ion exists in the pocket and binds to the O6 and N7 atoms of the two G bases and four phosphate groups. According to the previously-reported metal-binding properties to RNA molecules, many of divalent cations, such as Mg2+, Mn2+, Co2+, Zn2+, Ba2+, Pb2+ and Cd2+, may bind to the motif. This metal-binding motif can be used as a modular building block that allows for precise positioning of a single metal ion in functional nucleic acid molecules.

Canstatin inhibits hypoxia-induced apoptosis through activation of integrin/focal adhesion kinase/Akt signaling pathway in H9c2 cardiomyoblasts.

A hypoxic stress which causes apoptosis of cardiomyocytes is the main problem in the ischemic heart disease. Canstatin, a non-collagenous fragment of type IV collagen α2 chain, is an endogenous anti-angiogenic factor. We have previously reported that canstatin has a cytoprotective effect on cardiomyoblasts. In the present study, we examined the effects of canstatin on hypoxia-induced apoptosis in H9c2 cardiomyoblasts. Cell counting assay was performed to determine a cell viability. Western blotting was performed to detect expression of cleaved casepase-3 and phosphorylation of focal adhesion kinase (FAK) and Akt. Immunocytochemical staining was performed to observe a distribution of αv integrin. Hypoxia (1% O2, 48 h) significantly decreased cell viability and increased cleaved caspase-3 expression. Canstatin (10-250 ng/ml) significantly inhibited these changes in a concentration-dependent manner. Cilengitide (1 µM), an αvß3 and αvß5 integrin inhibitor, significantly prevented the protective effects of canstatin on cell viability. Canstatin significantly increased phosphorylation of FAK and Akt under hypoxic condition, which were inhibited by cilengitide. LY294002, an inhibitor of phosphatidylinositol-3 kinase/Akt pathway, suppressed the canstatin-induced Akt phosphorylation and reversed the protective effects of canstatin. It was observed that hypoxia caused a localization of αv integrin to focal adhesion. In summary, we for the first time clarified that canstatin inhibits hypoxia-induced apoptosis via FAK and Akt pathways through activating integrins in H9c2 cardiomyoblasts.

Structural insights into the catalytic reaction trigger and inhibition of D-3-hydroxybutyrate dehydrogenase.

D-3-Hydroxybutyrate dehydrogenase catalyzes the reversible conversion of acetoacetate and D-3-hydroxybutyrate. These ketone bodies are both energy-storage forms of acetyl-CoA. In order to clarify the structural mechanisms of the catalytic reaction with the cognate substrate D-3-hydroxybutyrate and of the inhibition of the reaction by inhibitors, the enzyme from Alcaligenes faecalis has been analyzed by X-ray crystallography in liganded states with the substrate and with two types of inhibitor: malonate and methylmalonate. In each subunit of the tetrameric enzyme, the substrate is trapped on the nicotinamide plane of the bound NAD(+). An OMIT map definitively shows that the bound ligand is D-3-hydroxybutyrate and not acetoacetate. The two carboxylate O atoms form four hydrogen bonds to four conserved amino-acid residues. The methyl group is accommodated in the nearby hydrophobic pocket so that the formation of a hydrogen bond from the OH group of the substrate to the hydroxy group of Tyr155 at the active centre is facilitated. In this geometry, the H atom attached to the C(3) atom of the substrate in the sp(3) configuration is positioned at a distance of 3.1 Šfrom the nicotinamide C(4) atom in the direction normal to the plane. In addition, the donor-acceptor relationship of the hydrogen bonds suggests that the Tyr155 OH group is allowed to ionize by the two donations from the Ser142 OH group and the ribose OH group. A comparison of the protein structures with and without ligands indicates that the Gln196 residue of the small movable domain participates in the formation of additional hydrogen bonds. It is likely that this situation can facilitate H-atom movements as the trigger of the catalytic reaction. In the complexes with inhibitors, however, their principal carboxylate groups interact with the enzyme in a similar way, while the interactions of other groups are changed. The crucial determinant for inhibition is that the inhibitors have no active H atom at C(3). A second determinant is the Tyr155 OH group, which is perturbed by the inhibitors to donate its H atom for hydrogen-bond formation, losing its nucleophilicity.

Toxicity modulation, resistance enzyme evasion, and A-site X-ray structure of broad-spectrum antibacterial neomycin analogs.

Aminoglycoside antibiotics are pseudosaccharides decorated with ammonium groups that are critical for their potent broad-spectrum antibacterial activity. Despite over three decades of speculation whether or not modulation of pKa is a viable strategy to curtail aminoglycoside kidney toxicity, there is a lack of methods to systematically probe amine-RNA interactions and resultant cytotoxicity trends. This study reports the first series of potent aminoglycoside antibiotics harboring fluorinated N1-hydroxyaminobutyryl acyl (HABA) appendages for which fluorine-RNA contacts are revealed through an X-ray cocrystal structure within the RNA A-site. Cytotoxicity in kidney-derived cells was significantly reduced for the derivative featuring our novel ß,ß-difluoro-HABA group, which masks one net charge by lowering the pKa without compromising antibacterial potency. This novel side-chain assists in evasion of aminoglycoside-modifying enzymes, and it can be easily transferred to impart these properties onto any number of novel analogs.

Magnetically tunable elasticity for magnetic hydrogels consisting of carrageenan and carbonyl iron particles.

A new class of magnetoelastic gel that demonstrates drastic and reversible changes in storage modulus without using strong magnetic fields was obtained. The magnetic gel consists of carrageenan and carbonyl iron particles. The magnetic gel with a volume fraction of magnetic particles of 0.30 exhibited a reversible increase by a factor of 1400 of the storage modulus upon a magnetic field of 500 mT, which is the highest value in the past for magnetorheological soft materials. It is considered that the giant magnetoelastic behavior is caused by both high dispersibility and high mobility of magnetic particles in the carrageenan gel. The off-field storage modulus of the magnetic gel at volume fractions below 0.30 obeyed the Krieger-Dougherty equation, indicating random dispersion of magnetic particles. At 500 mT, the storage modulus was higher than 4.0 MPa, which is equal to that of magnetic fluids, indicating that the magnetic particles move and form a chain structure by magnetic fields. Morphological study revealed the evidence that the magnetic particles embedded in the gel were aligned in the direction of magnetic fields, accompanied by stretching of the gel network. We conclude that the giant magnetoelastic phenomenon originates from the chain structure consisting of magnetic particles similar to magnetic fluids.