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author:("Tanaka, kiko")
1.  Cancer-associated retinopathy caused by benign thymoma 
doi:10.1136/bjo.2008.151563
PMCID: PMC3487380  PMID: 20424218
2.  Crystallization and preliminary crystallographic analysis of cyanide-insensitive alternative oxidase from Trypanosoma brucei brucei  
Cyanide-insensitive alternative oxidase from T. brucei brucei has been purified and crystallized for X-ray structure analysis.
Cyanide-insensitive alternative oxidase (AOX) is a mitochondrial membrane protein and a non-proton-pumping ubiquinol oxidase that catalyzes the four-electron reduction of dioxygen to water. In the African trypanosomes, tryp­anosome alternative oxidase (TAO) functions as a cytochrome-independent terminal oxidase that is essential for survival in the mammalian host; hence, the enzyme is considered to be a promising drug target for the treatment of trypanosomiasis. In the present study, recombinant TAO (rTAO) overexpressed in haem-deficient Escherichia coli was purified and crystallized at 293 K by the hanging-drop vapour-diffusion method using polyethylene glycol 400 as a precipitant. X-ray diffraction data were collected at 100 K and were processed to 2.9 Å resolution with 93.1% completeness and an overall R merge of 9.5%. The TAO crystals belonged to the orthorhombic space group I222 or I212121, with unit-cell parameters a = 63.11, b = 136.44, c = 223.06 Å. Assuming the presence of two rTAO molecules in the asymmetric unit (2 × 38 kDa), the calculated Matthews coefficient (V M) was 3.2 Å3 Da−1, which corresponds to a solvent content of 61.0%. This is the first report of a crystal of the membrane-bound diiron proteins, which include AOXs.
doi:10.1107/S1744309109054062
PMCID: PMC2833035  PMID: 20208159
alternative oxidases; membrane proteins; Trypanosoma brucei brucei; ascofuranone
3.  Overproduction, purification, crystallization and preliminary X-ray diffraction analysis of Trypanosoma brucei gambiense glycerol kinase 
Glycerol kinase from human African trypanosomes has been purified and crystallized for X-ray structure analysis.
In the bloodstream forms of human trypanosomes, glycerol kinase (GK; EC 2.7.1.30) is one of the nine glycosomally compartmentalized enzymes that are essential for energy metabolism. In this study, a recombinant Trypanosoma brucei gambiense GK (rTbgGK) with an N-terminal cleavable His6 tag was overexpressed, purified to homogeneity and crystallized by the sitting-drop vapour-diffusion method using PEG 400 as a precipitant. A complete X-ray diffraction data set to 2.75 Å resolution indicated that the crystals belonged to the orthorhombic space group P212121, with unit-cell parameters a = 63.84, b = 121.50, c = 154.59 Å. The presence of two rTbgGK molecules in the asymmetric unit gives a Matthews coefficient (V M) of 2.5 Å3 Da−1, corresponding to 50% solvent content.
doi:10.1107/S1744309110000369
PMCID: PMC2833043  PMID: 20208167
human African trypanosomiasis; Trypanosoma brucei gambiense; drug design; glycerol kinases
4.  Oral administration of PPC enhances antigen-specific CD8+ T cell responses while reducing IgE levels in sensitized mice 
Background
For almost 2000 years it has been recognized that aqueous extracts from pine cones possess medicinal properties beneficial for the treatment of a broad variety of diseases and conditions. In this report, the ability of an orally administered poly phenylpropanoid-polysaccharide rich extract of pine cones (PPC) to suppress the generation of IgE and to significantly enhance antigen-specific cellular responses to a variety of vaccines was tested.
Methods
A variety of vaccine protocols were utilized to determine the affects of orally administered PPC on the Th1/Th2 cytokine balance, the production of IgE antibodies, and the generation of antigen-specific cytotoxic T cells. The effect of PPC on the Th1/Th2 balance in aged mice was also investigated.
Results
Oral delivery of PPC was found to significantly suppress serum IgE levels in naïve mice and in mice sensitized to ovalbumin. PPC was also found to enhance the generation of antigen-specific CD8+ T cells in mice immunized with DNA, dendritic cell, and soluble protein vaccines. The suppression of IgE was associated with reduction of IL-4 secretion and the enhanced production of IL-12 and IFNγ by antigen-stimulated splenocytes from PPC treated mice. PPC also suppressed the Th2 response and enhanced the Th1 response of splenocytes from aged mice.
Conclusion
Oral delivery of PPC enhances the generation of an antigen-specific CD8+ T cell responses induced by soluble protein, DNA, and dendritic cell vaccines while at the same time suppressing the generation of a Th2 dominant IgE response. This effect on the Th1/Th2 balance was also observed in aged mice.
doi:10.1186/1472-6882-9-49
PMCID: PMC2794845  PMID: 19948039
5.  Purification, crystallization and preliminary X-ray diffraction study of human ribosomal protein L10 core domain 
A truncated variant of human ribosomal protien L10 was prepared and crystallized. Diffraction data were collected to 2.5 Å resolution.
Eukaryotic ribosomal protein L10 is an essential component of the large ribosomal subunit, which organizes the architecture of the aminoacyl-tRNA binding site. The human L10 protein is also called the QM protein and consists of 214 amino-acid residues. For crystallization, the L10 core domain (L10CD, Phe34–Glu182) was recombinantly expressed in Escherichia coli and purified to homogeneity. A hexagonal crystal of L10CD was obtained by the sitting-drop vapour-diffusion method. The L10CD crystal diffracted to 2.5 Å resolution and belongs to space group P3121 or P3221.
doi:10.1107/S1744309107048142
PMCID: PMC2339757  PMID: 18007048
ribsomal protein L10; core domain; QM protein; ribosome
6.  Purification, crystallization and preliminary X-ray diffraction of the C-terminal bromodomain from human BRD2 
The C-terminal bromodomain of human BRD2 was cloned, expressed, purified and crystallized. A complete diffraction data set has been collected to 1.80 Å resolution.
BRD2 is a bromodomain-containing BET-family protein that associates with acetylated histones throughout the cell cycle. Although the tertiary structures of the bromodomains involved in histone acetyl transfer are already known, the structures of the BET-type bromodomains, which are required for tight association with acetylated chromatin, are poorly understood. Here, the expression, purification and crystallization of the C-terminal bromodomain of human BRD2 are reported. The protein was crystallized by the sitting-drop vapour-diffusion method in the orthorhombic space group P21212, with unit-cell parameters a = 71.78, b = 52.60, c = 32.06 Å and one molecule per asymmetric unit. The crystal diffracted beyond 1.80 Å resolution using synchrotron radiation.
doi:10.1107/S1744309107028473
PMCID: PMC2335128  PMID: 17620725
acetylation; cell cycle; chromatin; gene expression; histones; transcription
7.  Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3 
Nucleic Acids Research  2009;37(15):5151-5166.
The CUG-binding protein 1 (CUG-BP1) is a member of the CUG-BP1 and ETR-like factors (CELF) family or the Bruno-like family and is involved in the control of splicing, translation and mRNA degradation. Several target RNA sequences of CUG-BP1 have been predicted, such as the CUG triplet repeat, the GU-rich sequences and the AU-rich element of nuclear pre-mRNAs and/or cytoplasmic mRNA. CUG-BP1 has three RNA-recognition motifs (RRMs), among which the third RRM (RRM3) can bind to the target RNAs on its own. In this study, we solved the solution structure of the CUG-BP1 RRM3 by hetero-nuclear NMR spectroscopy. The CUG-BP1 RRM3 exhibited a noncanonical RRM fold, with the four-stranded β-sheet surface tightly associated with the N-terminal extension. Furthermore, we determined the solution structure of the CUG-BP1 RRM3 in the complex with (UG)3 RNA, and discovered that the UGU trinucleotide is specifically recognized through extensive stacking interactions and hydrogen bonds within the pocket formed by the β-sheet surface and the N-terminal extension. This study revealed the unique mechanism that enables the CUG-BP1 RRM3 to discriminate the short RNA segment from other sequences, thus providing the molecular basis for the comprehension of the role of the RRM3s in the CELF/Bruno-like family.
doi:10.1093/nar/gkp546
PMCID: PMC2731918  PMID: 19553194
8.  Purification, crystallization and preliminary X-ray diffraction analysis of the non-ATPase subunit Nas6 in complex with the ATPase subunit Rpt3 of the 26S proteasome from Saccharomyces cerevisiae  
The complex of the non-ATPase subunit Nas6 with the C-terminal domain of the ATPase subunit Rpt3 of the 26S proteasome from S. cerevisiae was co-expressed in E. coli and purified to homogeneity. The crystals obtained from the protein complex diffracted to a resolution of 2.2 Å.
The non-ATPase subunit Nas6, which is the human orthologue of gankyrin, was co-expressed with the C-terminal domain of the ATPase subunit Rpt3 of the yeast 26S proteasome in Escherichia coli, purified to near-homogeneity and crystallized using the hanging-drop vapour-diffusion method. The protein crystallized in space group P21, with unit-cell parameters a = 60.38, b = 100.22, c = 72.20 Å, β = 94.70° and with three Nas6–Rpt3C molecules per asymmetric unit. The crystal diffracted to beyond 2.2 Å resolution using synchrotron radiation.
doi:10.1107/S1744309107004848
PMCID: PMC2330193  PMID: 17329811
Nas6; gankyrin; oncoproteins; Rpt3; proteasome; protein degradation; ubiquitin
9.  Crystallization of the archaeal transcription termination factor NusA: a significant decrease in twinning under microgravity conditions 
Crystallization of the transcription termination factor NusA under microgravity conditions significantly reduced the twinning content (1.0%) compared with terrestrially grown crystals (18.3%) and improved the maximum resolution from 3.0 to 2.29 Å, with similar unit-cell parameters.
The transcription termination factor NusA from Aeropyrum pernix was crystallized using a counter-diffusion technique in both terrestrial and microgravity environments. Crystallization under microgravity conditions significantly reduced the twinning content (1.0%) compared with terrestrially grown crystals (18.3%) and improved the maximum resolution from 3.0 to 2.29 Å, with similar unit-cell parameters. Based on a comparison of the crystal parameters, the effect of microgravity on protein crystallization is discussed.
doi:10.1107/S1744309106054625
PMCID: PMC2330117  PMID: 17277442
counter-diffusion; gel-tube method; hemihedral twinning; microgravity; transcription factors
10.  The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition 
Nucleic Acids Research  2008;36(14):4754-4767.
The degradation of the poly(A) tail is crucial for posttranscriptional gene regulation and for quality control of mRNA. Poly(A)-specific ribonuclease (PARN) is one of the major mammalian 3′ specific exo-ribonucleases involved in the degradation of the mRNA poly(A) tail, and it is also involved in the regulation of translation in early embryonic development. The interaction between PARN and the m7GpppG cap of mRNA plays a key role in stimulating the rate of deadenylation. Here we report the solution structures of the cap-binding domain of mouse PARN with and without the m7GpppG cap analog. The structure of the cap-binding domain adopts the RNA recognition motif (RRM) with a characteristic α-helical extension at its C-terminus, which covers the β-sheet surface (hereafter referred to as PARN RRM). In the complex structure of PARN RRM with the cap analog, the base of the N7-methyl guanosine (m7G) of the cap analog stacks with the solvent-exposed aromatic side chain of the distinctive tryptophan residue 468, located at the C-terminal end of the second β-strand. These unique structural features in PARN RRM reveal a novel cap-binding mode, which is distinct from the nucleotide recognition mode of the canonical RRM domains.
doi:10.1093/nar/gkn458
PMCID: PMC2504292  PMID: 18641416
11.  Purification, crystallization and preliminary X-ray diffraction analysis of the histone chaperone cia1 from fission yeast 
The histone chaperone cia1 from fission yeast has been overexpressed in E. coli, purified and crystallized using the vapour-diffusion method.
In fission yeast, cia1 + is an essential gene that encodes a histone chaperone, a homologue of human CIA (CCG1-interacting factor A) and budding yeast Asf1p (anti-silencing function-1), which both facilitate nucleosome assembly by interacting with the core histones H3/H4. The conserved domain (residues 1–­161) of the cia1 +-encoded protein was expressed in Escherichia coli, purified to near-homogeneity and crystallized by the sitting-drop vapour-diffusion method. The protein was crystallized in the monoclinic space group C2, with unit-cell parameters a = 79.16, b = 40.53, c = 69.79 Å, β = 115.93° and one molecule per asymmetric unit. The crystal diffracted to beyond 2.10 Å resolution using synchrotron radiation.
doi:10.1107/S1744309105030927
PMCID: PMC1978123  PMID: 16511210
gene silencing; nucleosome assembly; transcription
12.  Purification, crystallization and preliminary X-ray diffraction analysis of the Kelch-like motif region of mouse Keap1 
Keap1-DC (Kelch/double-glycine repeat and C-terminal region) of mouse Keap1 has been overexpressed in E. coli, purified and crystallized using the vapour-diffusion method.
Keap1 (Kelch-like ECH-associating protein 1) is a negative regulator of the Nrf2 transcription factor in the cytoplasm. The Kelch/DGR (double-glycine repeat) domain of Keap1 associates with Nrf2 as well as with actin filaments. A recombinant protein containing both the Kelch/DGR domain and the C-­terminal region of mouse Keap1 was expressed in Escherichia coli, purified to near-homogeneity and crystallized by the sitting-drop vapour-diffusion method. The crystal belongs to space group P61 or P65, with unit-cell parameters a = b = 102.95, c = 55.21 Å, and contains one molecule in the asymmetric unit. A complete diffraction data was collected to 2.25 Å resolution using an R-AXIS IV++ imaging plate mounted on an RA-Micro7 Cu Kα rotating-anode X-ray generator.
doi:10.1107/S1744309104032506
PMCID: PMC1952392  PMID: 16508120
Nrf2; transcription factor; Keap1; actin binding; antioxidants
13.  Separation of the Polypeptides of Chlamydia and Its Cell Walls by Polyacrylamide Gel Electrophoresis 
Journal of Bacteriology  1974;118(1):139-143.
The polypeptide composition of Chlamydia was examined by acrylamide gel electrophoresis. When the polypeptide patterns of purified infectious elementary bodies (EB) of C. psittaci meningopneumonitis strain, 6BC strain, and C. trachomatis T'ang strain were compared, no significant differences were observed. The polypeptide patterns of whole EB and reticulate bodies (RB) appeared to overlap, but differences were found. In EB cell walls, nine main and several minor bands of polypeptides were observed in gels containing sodium lauryl sulfate, and the eighth main band from the top of the gel stained positive with periodic acid-Schiff reagent. On the other hand, the polypeptides in bands 3, 6, and 8 in EB cell walls were missing or minor in RB cell walls, and the ninth band was clearly stained by PAS. Band 8 was also stained slightly. Purified subunits, which occur as a lattice structure on the inside layer of EB cell walls but are largely missing in RB cell walls, contained bands 4, 6, and 8, and band 8 was PAS positive. These results indicate that significant polypeptide synthesis or reorganization in the cell walls occurs during the growth cycle.
Images
PMCID: PMC246649  PMID: 4821091

Results 1-13 (13)