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author:("Lee, miha")
1.  Crystallization of a paraspeckle protein PSPC1–NONO heterodimer 
A truncated heterodimer of human PSPC1–NONO protein, a paraspeckle-specific complex, has been crystallized and the diffraction data collected to a resolution of 1.9 Å.
The paraspeckle component 1 (PSPC1) and non-POU-domain-containing octamer-binding protein (NONO) heterodimer is an essential structural component of paraspeckles, ribonucleoprotein bodies found in the interchromatin space of mammalian cell nuclei. PSPC1 and NONO both belong to the Drosophila behaviour and human splicing (DBHS) protein family, which has been implicated in many aspects of RNA processing. A heterodimer of the core DBHS conserved region of PSPC1 and NONO comprising two tandemly arranged RNA-recognition motifs (RRMs), a NONA/paraspeckle (NOPS) domain and part of a predicted coiled-coil domain has been crystallized in space group C2, with unit-cell parameters a = 90.90, b = 67.18, c = 94.08 Å, β = 99.96°. The crystal contained one heterodimer in the asymmetric unit and diffracted to 1.9 Å resolution using synchrotron radiation.
doi:10.1107/S1744309111026212
PMCID: PMC3212370  PMID: 22102035
paraspeckles; PSPC1–NONO heterodimer; RNA-recognition motifs; DBHS-family proteins
2.  Vasorelaxant Effect of Osterici Radix Ethanol Extract on Rat Aortic Rings 
The root of Ostericum koreanum Maximowicz has been used as a traditional medicine called “Kanghwal” in Korea (or “Qianghuo” in China). The purpose of this study was to investigate the vasorelaxant activity and mechanism of action of an ethanol extract of the O. koreanum root (EOK). We used isolated rat aortic rings to assess the effects of EOK on various vasorelaxant or vasoconstriction factors. EOK induced vasorelaxation in phenylephrine hydrochloride (PE) or KCl precontracted aortic rings in a concentration-dependent manner. However, the vasorelaxant effects of EOK on endothelium-intact aortic rings were reduced by pretreatment with L-NAME or methylene blue. In Ca2+-free Krebs-Henseleit solution, pretreatment with EOK (0.3 mg/mL) completely inhibited PE-induced constriction. In addition, EOK (0.3 mg/mL) also completely inhibited vasoconstriction induced by supplemental Ca2+ in aortic rings that were precontracted with PE or KCl. Furthermore, the EOK-induced vasorelaxation in PE-contracted aortic rings was inhibited by preincubation with nifedipine. These results indicate that the vasorelaxant effects of EOK are responsible for the induction of NO formation from L-Arg and NO-cGMP pathways, blockage of the extracellular Ca2+ entry via the receptor-operative Ca2+ channel and voltage-dependent calcium channel, and blockage of sarcoplasmic reticulum Ca2+ release via the inositol triphosphate pathway.
doi:10.1155/2013/350964
PMCID: PMC3800564  PMID: 24204390
3.  Vasorelaxant effect of Prunus yedoensis bark 
Background
Prunus yedoensis Matsum. is used as traditional medicine—‘Yaeng-Pi’ or ‘Hua-Pi’—in Japan and Korea. However, no studies have examined the pharmacological activities of the P. yedoensis bark. Only the antioxidant and antiviral activities of P. yedoensis fruit and the anti-hyperglycaemic effect of P. yedoensis leaf have been investigated. While studying the antihypertensive effects of several medicinal plants, we found that a methanol extract of P. yedoensis bark (MEPY) had distinct vasorelaxant effects on rat aortic rings.
Methods
The aortic rings were removed from Sprague–Dawley rats and suspended in organ chambers containing 10 ml Krebs-Henseleit solution. The aortic rings were placed between 2 tungsten stirrups and connected to an isometric force transducer. Changes in tension were recorded via isometric transducers connected to a data acquisition system.
Results
MEPY relaxed the contraction induced by phenylephrine (PE) both in endothelium-intact and endothelium-denuded aortic rings concentration dependently. However, the vasorelaxant effects of MEPY on endothelium-denuded aortic rings were lower than endothelium-intact aortic rings. The vasorelaxant effects of MEPY on endothelium-intact aortic rings were reduced by pre-treatment with l-NAME, methylene blue, or ODQ. However, pre-treatment with indomethacin, atropine, glibenclamide, tetraethylammonium, or 4-aminopyridine had no affection. In addition, MEPY inhibited the contraction induced by extracellular Ca2+ in endothelium-denuded rat thoracic aorta rings pre-contracted by PE (1 μM) or KCl (60 mM) in Ca2+-free solution.
Conclusions
Our results suggest that MEPY exerts its vasorelaxant effects via the activation of NO formation by means of l-Arg and NO-cGMP pathways and via the blockage of extracellular Ca2+ channels.
doi:10.1186/1472-6882-13-31
PMCID: PMC3585796  PMID: 23410148
4.  Inhibition of lipopolysaccharide-induced nitric oxide and prostaglandin E2 production by chloroform fraction of Cudrania tricuspidata in RAW 264.7 macrophages 
Background
Cudrania tricuspidata extract is an important traditional herbal remedy for tumors, inflammation, gastritis, and liver damage and is predominantly used in Korea, China, and Japan. However, the anti-inflammatory effects of the extract have not yet been conclusively proved.
Methods
In this study, we investigated the effects of the CHCl3 fraction (CTC) of a methanol extract of C. tricuspidata on the lipopolysaccharide (LPS)-induced nitric oxide (NO) and prostaglandin E2 (PGE2) production in RAW 264.7 macrophage cells and mouse peritoneal macrophages, and the levels of pro-inflammatory cytokines tumor necrosis factor-α (TNF-α), interleukin (IL)-1β and IL-6 in RAW 264.7 macrophage cells.
Results
We observed that the protein expression levels of inducible NO synthase and COX-2 enzymes were markedly inhibited by CTC in a concentration-dependent manner. In addition, CTC reduced the production of TNF-α, IL-1β, and IL-6 in the LPS-stimulated RAW 264.7 macrophage cells.
Conclusions
Our results show that the C. tricuspidata extract could modulate macrophage-mediated inflammatory functions such as the overproduction of cytokines, NO, and PGE2. The CTC was found to be the active fraction in this context.
doi:10.1186/1472-6882-12-250
PMCID: PMC3575384  PMID: 23228109
Cudrania tricuspidata; Nitric oxide; Prostaglandin E2; Lipopolysaccharide CHCl3 partitioned methanol extract of Cudrania tricuspidata; CTC, Lipopolysaccharide; LPS, prostaglandin E2; PGE2, nitric oxide; NO
5.  Crystallization of a ZRANB2–RNA complex 
The second RanBP2-type zinc finger from ZRANB2 has been crystallized in complex with a single-stranded RNA target sequence.
ZRANB2 is a zinc-finger protein that has been shown to influence alternative splice-site selection. The protein comprises a C-terminal arginine/serine-rich domain that interacts with spliceosomal proteins and two N-terminal RanBP2-type zinc fingers that have been implicated in RNA recognition. The second zinc finger bound to a six-nucleotide single-stranded RNA target sequence crystallized in the hexagonal space group P6522 or P6122, with unit-cell parameters a = 54.52, b = 54.52, c = 48.07 Å; the crystal contains one monomeric complex per asymmetric unit. This crystal form has a solvent content of 39% and diffracted to 1.4 Å resolution using synchrotron radiation.
doi:10.1107/S1744309108036993
PMCID: PMC2593708  PMID: 19052380
RanBP2-type zinc fingers; RNA-binding proteins; splicing factors
6.  Crystallization of an Lhx3–Isl1 complex 
An intramolecular complex comprising the LIM domains of Lhx3 and the interacting domain of Isl1 tethered by a flexible linker was engineered, overexpressed in E. coli, purified and crystallized.
A stable intramolecular complex comprising the LIM domains of the LIM-homeodomain protein Lhx3 tethered to a peptide region of Isl1 has been engineered, purified and crystallized. The monoclinic crystals belong to space group C2, with unit-cell parameters a = 119, b = 62.2, c = 51.9 Å, β = 91.6°, and diffract to 2.05 Å resolution.
doi:10.1107/S174430910800691X
PMCID: PMC2374238  PMID: 18391431
Lhx3; Isl1; LIM-homeodomain proteins; protein complex; motor-neuron development
7.  Structure of the T109S mutant of Escherichia coli dihydroorotase complexed with the inhibitor 5-­fluoroorotate: catalytic activity is reflected by the crystal form 
A single-point mutant (T109S) of E. coli dihydroorotase initially crystallizes so that the two monomers of the dimer are related by a crystallographic twofold axis. In the presence of substrate, conversion to the previously observed asymmetric dimer with substrate bound in one subunit and product in the other is observed.
Crystals of a single-point mutant (T109S) of Escherichia coli dihydroorotase (DHOase) with diminished activity grown in the presence of l-dihydroorotate (l-DHO) are tetragonal, with a monomer in the asymmetric unit. These crystals are extremely unstable and disintegrate shortly after formation, which is followed by the growth of orthorhombic crystals from the remnants of the tetragonal crystals or at new nucleation sites. Orthorhombic crystals, for which a structure has previously been reported [Thoden et al. (2001 ▶), Biochemistry, 40, 6989–6997; Lee et al. (2005 ▶), J. Mol. Biol. 348, 523–533], contain a dimer of DHOase in the asymmetric unit; the active site of one monomer contains the substrate N-carbamyl-l-aspartate (l-CA-asp) and the active site of the other monomer contains the product of the reaction, l-DHO. In the subunit with l-­DHO in the active site, a surface loop (residues 105–115) is ‘open’. In the other subunit, with l-CA-asp in the active site, the loop folds inwards, forming specific hydrogen bonds from the loop to the l-CA-asp. The tetragonal crystal form can be stabilized by crystallization in the presence of the inhibitor 5-fluoroorotate (FOA), a product (l-DHO) mimic. Crystals of the complex of T109S DHOase with FOA are tetragonal, space group P41212, with unit-cell parameters a = b = 72.6, c = 176.1 Å. The structure has been refined to R and R free values of 0.218 and 0.257, despite severe anisotropy of the diffraction. In this structure, the flexible loops are both in the ‘open’ conformation, which is consistent with FOA, like l-­DHO, binding at both sites. The behaviour of the T109S mutant crystals of DHOase in the presence of l-DHO is explained by initial binding of l-DHO to both subunits, followed by slow conversion to l-CA-asp, with consequent movement of the flexible loop and dissolution of the crystals. Orthorhombic crystals are then able to grow in the presence of l-DHO and l-CA-asp.
doi:10.1107/S1744309107004009
PMCID: PMC2330171  PMID: 17329804
dihydroorotase; conformational change; loop movement; catalytic state; crystal contacts; crystal instability

Results 1-7 (7)