Genomes and Genes
Experts and Doctors on amino acid sequence in Yokohama, Kanagawa, Japan
Locale: Yokohama, Kanagawa, Japan
Topic: amino acid sequence
Publications165 found, 100 shown here
- Kagawa W, Kurumizaka H, Ishitani R, Fukai S, Nureki O, Shibata T, et al. Crystal structure of the homologous-pairing domain from the human Rad52 recombinase in the undecameric form. Mol Cell. 2002;10:359-71 pubmed..A mutational analysis revealed that the amino acid residues located between the beta-beta-beta-alpha fold and the characteristic hairpin loop are essential for ssDNA and dsDNA binding. ..
- Wada T, Shirouzu M, Terada T, Ishizuka Y, Matsuda T, Kigawa T, et al. Structure of a conserved CoA-binding protein synthesized by a cell-free system. Acta Crystallogr D Biol Crystallogr. 2003;59:1213-8 pubmed..An isothermal titration calorimetry experiment was performed to investigate whether TT1466 binds CoA and revealed high-affinity CoA binding of TT1466. ..
- Suno R, Taguchi H, Masui R, Odaka M, Yoshida M. Trigger factor from Thermus thermophilus is a Zn2+-dependent chaperone. J Biol Chem. 2004;279:6380-4 pubmed..5 mol Zn2+/mol TF. The folding-arrest activity of TF that was saturated with Zn2+ (approximately 1 mol/mol TF) was twice as efficient as that of untreated TF. Thus, chaperone activity of thermophilic TF is Zn2+-dependent. ..
- Kudo H, Amizuka N, Araki K, Inohaya K, Kudo A. Zebrafish periostin is required for the adhesion of muscle fiber bundles to the myoseptum and for the differentiation of muscle fibers. Dev Biol. 2004;267:473-87 pubmed
- Matsubara T, Iijima K, Nakamura M, Taki T, Okahata Y, Sato T. Specific binding of GM1-binding peptides to high-density GM1 in lipid membranes. Langmuir. 2007;23:708-14 pubmed..The GM1-binding peptide played a role as a unique anti-GM1 probe differing from the cholera toxin B subunit or antibodies. ..
- Dong X, Kato Murayama M, Muramatsu T, Mori H, Shirouzu M, Bessho Y, et al. The crystal structure of leucyl/phenylalanyl-tRNA-protein transferase from Escherichia coli. Protein Sci. 2007;16:528-34 pubmed..The conserved residues in the central cavity of L/F-transferase suggest that this region is important for the enzyme catalysis. ..
- Nakamura Y, Nakano K, Umehara T, Kimura M, Hayashizaki Y, Tanaka A, et al. Structure of the oncoprotein gankyrin in complex with S6 ATPase of the 26S proteasome. Structure. 2007;15:179-89 pubmed..These results provide a structural basis for the involvement of gankyrin in the pRb degradation pathway, through its association with S6 ATPase of the 26S proteasome. ..
- Doi Katayama Y, Hayashi F, Inoue M, Yabuki T, Aoki M, Seki E, et al. Solution structure of the general transcription factor 2I domain in mouse TFII-I protein. Protein Sci. 2007;16:1788-92 pubmed
- Yamasaki S, Ishikawa E, Sakuma M, Hara H, Ogata K, Saito T. Mincle is an ITAM-coupled activating receptor that senses damaged cells. Nat Immunol. 2008;9:1179-88 pubmed publisher..Our results suggest that Mincle is a receptor that senses nonhomeostatic cell death and thereby induces the production of inflammatory cytokines to drive the infiltration of neutrophils into damaged tissue. ..
- Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S. Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N(epsilon)-(o-azidobenzyloxycarbonyl) lysine for site-specific protein modification. Chem Biol. 2008;15:1187-97 pubmed publisher..The AzZLys-containing protein was labeled with a fluorescent probe, by Staudinger ligation...
- Matsubara T, Sumi M, Kubota H, Taki T, Okahata Y, Sato T. Inhibition of influenza virus infections by sialylgalactose-binding peptides selected from a phage library. J Med Chem. 2009;52:4247-56 pubmed publisher..Carbohydrate-binding peptides that inhibit carbohydrate-virus interaction showed inhibitory activity. These results may lead to a new approach to the design of antiviral drugs. ..
- Nakanishi J, Yamamoto M, Koyama J, Sato J, Hibino T. Keratinocytes synthesize enteropeptidase and multiple forms of trypsinogen during terminal differentiation. J Invest Dermatol. 2010;130:944-52 pubmed publisher..Because mesotrypsin is resistant to naturally occurring trypsin inhibitors, confined expression of the isoforms of mesotrypsinogens and enteropeptidase may indicate that mesotrypsin is involved in keratinocyte terminal differentiation. ..
- Nagata T, Niyada E, Fujimoto N, Nagasaki Y, Noto K, Miyanoiri Y, et al. Solution structures of the trihelix DNA-binding domains of the wild-type and a phosphomimetic mutant of Arabidopsis GT-1: mechanism for an increase in DNA-binding affinity through phosphorylation. Proteins. 2010;78:3033-47 pubmed publisher..On the basis of our findings, we propose a mechanism by which the DNA-binding activity toward BoxII of the phosphorylated GT-1 could be enhanced. ..
- Sakai H, Suzuki S, Mizuguchi T, Imoto K, Yamashita Y, Doi H, et al. Rapid detection of gene mutations responsible for non-syndromic aortic aneurysm and dissection using two different methods: resequencing microarray technology and next-generation sequencing. Hum Genet. 2012;131:591-9 pubmed publisher..Next-generation sequencing was able to detect almost all types of mutation, but requires improved informatics methods. ..
- Tsuganezawa K, Shinohara Y, Ogawa N, Tsuboi S, Okada N, Mori M, et al. Two-colored fluorescence correlation spectroscopy screening for LC3-P62 interaction inhibitors. J Biomol Screen. 2013;18:1103-9 pubmed publisher..The two-colored FCS-based screening was shown to be effective to screen for protein-protein interaction inhibitors. ..
- Nakamura T, Sanokawa R, Sasaki Y, Ayusawa D, Oishi M, Mori N. Cyclin I: a new cyclin encoded by a gene isolated from human brain. Exp Cell Res. 1995;221:534-42 pubmed..The expression of cyclin I mRNA does not correlate directly to the cell cycle, and therefore cyclin I may be a novel cyclin member that functions independently of the cell cycle control. ..
- Itakura M, Iwashina M, Mizuno T, Ito T, Hagiwara H, Hirose S. Mutational analysis of disulfide bridges in the type C atrial natriuretic peptide receptor. J Biol Chem. 1994;269:8314-8 pubmed
- Iwasaki T, Wakagi T, Oshima T. Resolution of the aerobic respiratory system of the thermoacidophilic archaeon, Sulfolobus sp. strain 7. III. The archaeal novel respiratory complex II (succinate:caldariellaquinone oxidoreductase complex) inherently lacks heme group. J Biol Chem. 1995;270:30902-8 pubmed..This further indicates that the heme group of several respiratory complexes II may not be involved in the redox intermediates of the electron transfer from succinate to quinone...
- Kuroiwa Y, Kaneko ishino T, Kagitani F, Kohda T, Li L, Tada M, et al. Peg3 imprinted gene on proximal chromosome 7 encodes for a zinc finger protein. Nat Genet. 1996;12:186-90 pubmed..This region is syntenic with human chromosome 19q13.1-13.3 (refs 10,11), where the genes for myotonic dystrophy and a putative tumour suppressor gene are located. ..
- Suzuki T, Inoki Y, Yamagishi A, Iwasaki T, Wakagi T, Oshima T. Molecular and phylogenetic characterization of isopropylmalate dehydrogenase of a thermoacidophilic archaeon, Sulfolobus sp. strain 7. J Bacteriol. 1997;179:1174-9 pubmed..These results suggested that the present enzyme is the most primitive among isopropylmalate dehydrogenases belonging in the decarboxylating dehydrogenase family. ..
- Motohashi K, Yohda M, Odaka M, Yoshida M. K+ is an indispensable cofactor for GrpE stimulation of ATPase activity of DnaK x DnaJ complex from Thermus thermophilus. FEBS Lett. 1997;412:633-6 pubmed..Using proteins of this bacterium, we found that the GrpE stimulation of ATPase activity of DnaK x DnaJ complex was absolutely dependent on the presence of K+. ..
- Sasai H, Masaki M, Wakitani K. Suppression of polypogenesis in a new mouse strain with a truncated Apc(Delta474) by a novel COX-2 inhibitor, JTE-522. Carcinogenesis. 2000;21:953-8 pubmed..These results suggest that COX-2 plays an important role in polypogenesis and COX-2-selective inhibitors can be used as new preventive therapeutics against colorectal tumors. ..
- Umitsuki G, Wachi M, Takada A, Hikichi T, Nagai K. Involvement of RNase G in in vivo mRNA metabolism in Escherichia coli. Genes Cells. 2001;6:403-10 pubmed..5-fold longer in the rng:cat disruptant than in the wild-type. These results indicate that, in addition to rRNA processing, RNase G is involved in in vivo mRNA degradation in E. coli. ..
- Yamashita A, Ohnishi T, Kashima I, Taya Y, Ohno S. Human SMG-1, a novel phosphatidylinositol 3-kinase-related protein kinase, associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay. Genes Dev. 2001;15:2215-28 pubmed..Taken together, we conclude that hSMG-1 plays a critical role in NMD through the direct phosphorylation of hUPF1/SMG-2 in the evolutionally conserved mRNA surveillance complex. ..
- Akanuma S, Kigawa T, Yokoyama S. Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set. Proc Natl Acad Sci U S A. 2002;99:13549-53 pubmed..Therefore, the catalytic function associated with a relatively large protein may be achieved with a subset of the 20 amino acid. The converged sequence also implies simpler constituents for proteins in the early stage of evolution. ..
- Bando M, Hasegawa M, Tsuboi Y, Miyake Y, Shiina M, Ito M, et al. The mycotoxin penicillic acid inhibits Fas ligand-induced apoptosis by blocking self-processing of caspase-8 in death-inducing signaling complex. J Biol Chem. 2003;278:5786-93 pubmed..Thus, our present results demonstrate that PCA inhibits FasL-induced apoptosis by targeting self-processing of caspase-8...
- Yazawa T, Ishii H, Ito T, Yoshiike Y, Ogawa N, Okudela K, et al. Colliding primary lung cancers of adenosquamous carcinoma and large cell neuroendocrine carcinoma. Pathol Int. 2003;53:58-65 pubmed..From these clinical and pathological results, the parental cell of the large cell neuroendocrine carcinomatous element was considered to be different from that of the adenosquamous carcinomatous element...
- Tanaka Y, Kaneko S, Katsukawa S, Yamazaki T, Ohta A, Miyazaki Y, et al. Specific distribution in homobasidiomycete hymenophores of the transcripts of Ras protein and G-protein alpha-subunit genes. FEMS Microbiol Lett. 2005;242:169-75 pubmed..This suggests that the ras and ga1 genes play distinct physiological roles in the hymenophores of both basidiomycete fungi. ..
- Nemoto Y, Higuchi K, Baba O, Kudo A, Takano Y. Multinucleate osteoclasts in medaka as evidence of active bone remodeling. Bone. 2007;40:399-408 pubmed..These results suggest the feasibility of medaka as a model animal for the investigation of bone-related abnormalities and their genetic backgrounds. ..
- Maruyama Nakashita A, Nakamura Y, Tohge T, Saito K, Takahashi H. Arabidopsis SLIM1 is a central transcriptional regulator of plant sulfur response and metabolism. Plant Cell. 2006;18:3235-51 pubmed
- Heddle J, Okajima T, Scott D, Akashi S, Park S, Tame J. Dynamic allostery in the ring protein TRAP. J Mol Biol. 2007;371:154-67 pubmed publisher..We have identified a single, conservative amino acid replacement (Ile to Leu) in B. subtilis TRAP that abolishes this effect, and suggest the initial ligand binding causes a change throughout the wild-type protein ring...
- Shishido K, Nobusaka R, Kaneko S, Sato Y, Akiyama R, Miyazaki Y, et al. Long terminal repeat of the mushroom retrotransposon functions as a dual terminator to transcription. Biosci Biotechnol Biochem. 2007;71:2321-4 pubmed
- Tominaga R, Iwata M, Sano R, Inoue K, Okada K, Wada T. Arabidopsis CAPRICE-LIKE MYB 3 (CPL3) controls endoreduplication and flowering development in addition to trichome and root hair formation. Development. 2008;135:1335-45 pubmed publisher..Notably, the CPL3 gene has pleiotropic effects on flowering development, epidermal cell size and trichome branching through the regulation of endoreduplication. ..
- Kuwasako K, Takahashi M, Tochio N, Abe C, Tsuda K, Inoue M, et al. Solution structure of the second RNA recognition motif (RRM) domain of murine T cell intracellular antigen-1 (TIA-1) and its RNA recognition mode. Biochemistry. 2008;47:6437-50 pubmed publisher..An investigation of the chemical shift perturbation revealed similarity in the RNA recognition modes between the TIA-1 and U2AF65 RRMs. ..
- Nakachi M, Hoshi M, Matsumoto M, Moriyama H. Conserved sequences of sperm-activating peptide and its receptor throughout evolution, despite speciation in the sea star Asterias amurensis and closely related species. Zygote. 2008;16:229-37 pubmed publisher..Although the sperm-activating peptide and its receptor share certain common sequences, they may serve as barriers that ensure speciation in the sea star A. amurensis and closely related species...
- Takayama H, Sugio S. Functional expression of milligram quantities of the synthetic human serotonin transporter gene in a tetracycline-inducible HEK293 cell line. Protein Expr Purif. 2011;76:211-20 pubmed publisher..Our expression platform using synthetic codon-optimized gene and mammalian stable cell lines is feasible to produce milligram-scale functional membrane transporter for further biophysical and biochemical studies. ..
- Muramatsu T, Kim Y, Nishii W, Terada T, Shirouzu M, Yokoyama S. Autoprocessing mechanism of severe acute respiratory syndrome coronavirus 3C-like protease (SARS-CoV 3CLpro) from its polyproteins. FEBS J. 2013;280:2002-13 pubmed publisher..A numerical simulation of the maturation pathway is presented. ..
- Saitsu H, Fukai R, Ben Zeev B, Sakai Y, Mimaki M, Okamoto N, et al. Phenotypic spectrum of GNAO1 variants: epileptic encephalopathy to involuntary movements with severe developmental delay. Eur J Hum Genet. 2016;24:129-34 pubmed publisher..Our study demonstrated that GNAO1 variants can cause involuntary movements and severe developmental delay with/without seizures, including various types of early-onset epileptic encephalopathy. ..
- Kaneko ishino T, Kuroiwa Y, Miyoshi N, Kohda T, Suzuki R, Yokoyama M, et al. Peg1/Mest imprinted gene on chromosome 6 identified by cDNA subtraction hybridization. Nat Genet. 1995;11:52-9 pubmed..Peg1/Mest is widely expressed in mesodermal tissues and belongs to the alpha/beta hydrolase fold family. A similar approach with androgenones can be used to identify imprinted genes that are expressed from the maternal genome only. ..
- Nagata K, Kawase H, Handa H, Yano K, Yamasaki M, Ishimi Y, et al. Replication factor encoded by a putative oncogene, set, associated with myeloid leukemogenesis. Proc Natl Acad Sci U S A. 1995;92:4279-83 pubmed..Studies with mutant TAF-I proteins devoid of this acidic region indicated that the acidic region is essential for TAF-I activity. ..
- Takezawa R, Shinzawa K, Watanabe Y, Akaike T. Determination of mouse major asialoglycoprotein receptor cDNA sequence. Biochim Biophys Acta. 1993;1172:220-2 pubmed..According to the homology analysis, we concluded that the clone encodes the mouse major asialoglycoprotein receptor (MHL-1). ..
- Osada S, Izawa M, Saito R, Mizuno K, Suzuki A, Hirai S, et al. YSK1, a novel mammalian protein kinase structurally related to Ste20 and SPS1, but is not involved in the known MAPK pathways. Oncogene. 1997;14:2047-57 pubmed..These results suggest that YSK1 may be involved in the regulation of a novel intracellular signaling pathway. ..
- Yokoyama M, Nakamura M, Okubo K, Matsubara K, Nishi Y, Matsumoto T, et al. Isolation of a cDNA encoding a widely expressed novel zinc finger protein with the LeR and KRAB-A domains. Biochim Biophys Acta. 1997;1353:13-7 pubmed..A cross-species genomic hybridization indicates that the FPM315 gene is highly conserved among eukaryotes. These data suggest that FPM315 might play an important role in basic cellular processes. ..
- Fujii M, Ishii N, Joguchi A, Yasuda K, Ayusawa D. A novel superoxide dismutase gene encoding membrane-bound and extracellular isoforms by alternative splicing in Caenorhabditis elegans. DNA Res. 1998;5:25-30 pubmed..It is, therefore, indicated that SOD4-1 is an extracellular form and SOD4-2 a membrane-bound form, the latter representing a novel type of SOD. In C. elegans, SOD4-2 mRNA was found to be preferentially expressed in eggs. ..
- Qu C, Akanuma S, Tanaka N, Moriyama H, Oshima T. Design, X-ray crystallography, molecular modelling and thermal stability studies of mutant enzymes at site 172 of 3-isopropylmalate dehydrogenase from Thermus thermophilus. Acta Crystallogr D Biol Crystallogr. 2001;57:225-32 pubmed
- Okumura E, Fukuhara T, Yoshida H, Hanada Si S, Kozutsumi R, Mori M, et al. Akt inhibits Myt1 in the signalling pathway that leads to meiotic G2/M-phase transition. Nat Cell Biol. 2002;4:111-6 pubmed..These findings identify Myt1 as a new target of Akt, and demonstrate that Akt functions as an M-phase initiator. ..
- Ideguchi H, Ueda A, Tanaka M, Yang J, Tsuji T, Ohno S, et al. Structural and functional characterization of the USP11 deubiquitinating enzyme, which interacts with the RanGTP-associated protein RanBPM. Biochem J. 2002;367:87-95 pubmed..Finally, ubiquitin conjugation to RanBPM was inhibited in a dose-dependent manner by the addition of recombinant USP11. We conclude that RanBPM was the enzymic substrate for USP11 and was deubiquitinated specifically. ..
- Sakai H, Kajiwara S. A stearoyl-CoA-specific Delta 9 fatty acid desaturase from the basidiomycete Lentinula edodes. Biosci Biotechnol Biochem. 2003;67:2431-7 pubmed..edodes were higher than in mycelia cultivated at 18 degrees C as well as 25 degrees C. These results correlated with the increase of unsaturated fatty acids (UFAs) in total lipids during fruiting-body formation. ..
- Kurimoto K, Muto Y, Obayashi N, Terada T, Shirouzu M, Yabuki T, et al. Crystal structure of the N-terminal RecA-like domain of a DEAD-box RNA helicase, the Dugesia japonica vasa-like gene B protein. J Struct Biol. 2005;150:58-68 pubmed..Therefore, the structural features that we found are characteristic of the PL10-subfamily proteins and might contribute to their biological roles in germ-line development. ..
- Kurochkin I, Nagashima T, Konagaya A, Schonbach C. Sequence-based discovery of the human and rodent peroxisomal proteome. Appl Bioinformatics. 2005;4:93-104 pubmed
- Adachi M, Tachibana K, Asakura Y, Tsuchiya T. A novel mutation in the GATA3 gene in a family with HDR syndrome (Hypoparathyroidism, sensorineural Deafness and Renal anomaly syndrome). J Pediatr Endocrinol Metab. 2006;19:87-92 pubmed..The present findings lend additional support to the notion that the phenotype cannot be precisely estimated from the genotype in HDR syndrome. ..
- Takahata S, Ida T, Senju N, Sanbongi Y, Miyata A, Maebashi K, et al. Horizontal gene transfer of ftsI, encoding penicillin-binding protein 3, in Haemophilus influenzae. Antimicrob Agents Chemother. 2007;51:1589-95 pubmed..In conclusion, horizontal transfer of the ftsI gene in H. influenzae can occur in an intraspecies and an interspecies manner. ..
- Iizumi Y, Sagara H, Kabe Y, Azuma M, Kume K, Ogawa M, et al. The enteropathogenic E. coli effector EspB facilitates microvillus effacing and antiphagocytosis by inhibiting myosin function. Cell Host Microbe. 2007;2:383-92 pubmed..These results suggest that EspB inhibits myosin functions and thereby facilitates efficient infection by EPEC. ..
- Okuda M, Tanaka A, Satoh M, Mizuta S, Takazawa M, Ohkuma Y, et al. Structural insight into the TFIIE-TFIIH interaction: TFIIE and p53 share the binding region on TFIIH. EMBO J. 2008;27:1161-71 pubmed publisher..From our in vitro studies, we demonstrate that this interaction could be a switch to replace p53 with TFIIE on TFIIH in transcription. ..
- Tsunezumi J, Higashi S, Miyazaki K. Matrilysin (MMP-7) cleaves C-type lectin domain family 3 member A (CLEC3A) on tumor cell surface and modulates its cell adhesion activity. J Cell Biochem. 2009;106:693-702 pubmed publisher..It can be speculated that the cleavage of CLEC3A by MMP-7 weakens the stable adhesion of tumor cells to the matrix and promotes their migration in tumor microenvironments. ..
- Sano H, Kaneko S, Sakamoto Y, Sato T, Shishido K. The basidiomycetous mushroom Lentinula edodes white collar-2 homolog PHRB, a partner of putative blue-light photoreceptor PHRA, binds to a specific site in the promoter region of the L. edodes tyrosinase gene. Fungal Genet Biol. 2009;46:333-41 pubmed publisher..The expression of phrB and Le.tyr genes in pre-primordial mycelia of L. edodes is induced by light exposure, suggesting that PHRB can regulate the expression of the Le.tyr gene in a light-dependent manner. ..
- Sugiyama K, Obayashi E, Kawaguchi A, Suzuki Y, Tame J, Nagata K, et al. Structural insight into the essential PB1-PB2 subunit contact of the influenza virus RNA polymerase. EMBO J. 2009;28:1803-11 pubmed publisher..This novel interface is surprisingly small, yet, it has a crucial function in regulating the 250 kDa polymerase complex and is completely conserved among avian and human influenza viruses. ..
- He F, Saito K, Kobayashi N, Harada T, Watanabe S, Kigawa T, et al. Structural and functional characterization of the NHR1 domain of the Drosophila neuralized E3 ligase in the notch signaling pathway. J Mol Biol. 2009;393:478-95 pubmed publisher..The present structural study will shed light on the role of the Neur NHR1 domain in the Notch signaling pathway. ..
- Malay A, Bessho Y, Ellis M, Antonyuk S, Strange R, Hasnain S, et al. Structure of glyceraldehyde-3-phosphate dehydrogenase from the archaeal hyperthermophile Methanocaldococcus jannaschii. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009;65:1227-33 pubmed publisher..The key phosphate-binding residues in the active site of Mj-GAPDH are conserved in other archaeal GAPDH proteins. These residues undergo a conformational shift in response to occupancy of the inorganic phosphate site...
- He F, Umehara T, Saito K, Harada T, Watanabe S, Yabuki T, et al. Structural insight into the zinc finger CW domain as a histone modification reader. Structure. 2010;18:1127-39 pubmed publisher..Our structural and biochemical studies have identified the zf-CW domain as a member of the histone modification reader modules for epigenetic regulation. ..
- Kondo Y, Saitsu H, Miyamoto T, Lee B, Nishiyama K, Nakashima M, et al. Pathogenic mutations in two families with congenital cataract identified with whole-exome sequencing. Mol Vis. 2013;19:384-9 pubmed..WES will be the first choice for clinical services in the near future, providing useful information for genetic counseling and family planning. ..
- Wada T, Takagi T, Yamaguchi Y, Ferdous A, Imai T, Hirose S, et al. DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes Dev. 1998;12:343-56 pubmed..The combination of biochemical studies on DSIF and genetic analysis of Spt4 and Spt5 in yeast, also in this issue, indicates that DSIF associates with RNA Pol II and regulates its processivity in vitro and in vivo. ..
- Miya T, Nishida H. An Ets transcription factor, HrEts, is target of FGF signaling and involved in induction of notochord, mesenchyme, and brain in ascidian embryos. Dev Biol. 2003;261:25-38 pubmed..These results suggest that an Ets transcription factor, HrEts, is involved in signal transduction of FGF commonly in notochord, mesenchyme, and brain induction in ascidian embryos. ..
- Honda S, Aihara T, Hontani M, Okubo K, Hirose S. Mutational analysis of action of mitochondrial fusion factor mitofusin-2. J Cell Sci. 2005;118:3153-61 pubmed
- Matsumoto Y, Murai M, Fujita D, Sakamoto K, Miyoshi H, Yoshida M, et al. Mass spectrometric analysis of the ubiquinol-binding site in cytochrome bd from Escherichia coli. J Biol Chem. 2006;281:1905-12 pubmed
- Shinohara H, Yasuda T, Aiba Y, Sanjo H, Hamadate M, Watarai H, et al. PKC beta regulates BCR-mediated IKK activation by facilitating the interaction between TAK1 and CARMA1. J Exp Med. 2005;202:1423-31 pubmed..Hence, our data suggest that phosphorylation of CARMA1, mediated by PKCbeta, brings two key protein kinases, TAK1 and IKK, into close proximity, thereby allowing TAK1 to phosphorylate IKK. ..
- Kukimoto Niino M, Yoshikawa S, Takagi T, Ohsawa N, Tomabechi Y, Terada T, et al. Crystal structure of the Ca²⁺/calmodulin-dependent protein kinase kinase in complex with the inhibitor STO-609. J Biol Chem. 2011;286:22570-9 pubmed publisher..Therefore, the present structure provides a molecular basis for clarifying the known biochemical properties of CaMKKβ and for designing novel inhibitors targeting CaMKKβ and the related protein kinases. ..
- Matsuno H, Niikura K, Okahata Y. Design and characterization of asparagine- and lysine-containing alanine-based helical peptides that bind selectively to A.T base pairs of oligonucleotides immobilized on a 27 mhz quartz crystal microbalance. Biochemistry. 2001;40:3615-22 pubmed..T base pairs (K(a) = 5.9 x 10(5) M(-1)) than for G.C base pairs (K(a) = 1.2 x 10(5) M(-1)), and alpha-helices were clearly promoted by the binding to A.T base pairs from CD spectral changes. ..
- Kasai T, Inoue M, Koshiba S, Yabuki T, Aoki M, Nunokawa E, et al. Solution structure of a BolA-like protein from Mus musculus. Protein Sci. 2004;13:545-8 pubmed..This fold is similar to the class II KH fold, except for the absence of the GXXG loop, which is well conserved in the KH fold. The conserved residues in the BolA-like proteins are assembled on the one side of the protein. ..
- Mizutani K, Machida Y, Unzai S, Park S, Tame J. Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli. Biochemistry. 2004;43:4454-63 pubmed..Despite the conserved topology shared by the two proteins, the surface shape and charge distribution are very different. The models suggest significant differences in substrate binding by different pseudouridine synthases. ..
- Hiraoka D, Hori Oshima S, Fukuhara T, Tachibana K, Okumura E, Kishimoto T. PDK1 is required for the hormonal signaling pathway leading to meiotic resumption in starfish oocytes. Dev Biol. 2004;276:330-6 pubmed..They further support that PDK2 is a molecule distinct from PDK1 and Akt, and that PDK2 activity is not sufficient for the full activation of Akt in the absence of PDK1 activity...
- Morokuma Y, Nakamura N, Kato A, Notoya M, Yamamoto Y, Sakai Y, et al. MARCH-XI, a novel transmembrane ubiquitin ligase implicated in ubiquitin-dependent protein sorting in developing spermatids. J Biol Chem. 2007;282:24806-15 pubmed..Our data suggest that MARCH-XI acts as a ubiquitin ligase with a role in ubiquitin-mediated protein sorting in the TGN-MVB transport pathway, which may be involved in mammalian spermiogenesis. ..
- Aihara T, Nakamura N, Honda S, Hirose S. A novel potential role for gametogenetin-binding protein 1 (GGNBP1) in mitochondrial morphogenesis during spermatogenesis in mice. Biol Reprod. 2009;80:762-70 pubmed publisher..These results suggest that GGNBP1 is involved in spermatogenesis by modifying mitochondrial dynamics and morphology. ..
- Hara K, Hashimoto H, Murakumo Y, Kobayashi S, Kogame T, Unzai S, et al. Crystal structure of human REV7 in complex with a human REV3 fragment and structural implication of the interaction between DNA polymerase zeta and REV1. J Biol Chem. 2010;285:12299-307 pubmed publisher..Our results will provide a general structural basis for understanding the REV7 interaction. ..
- Yoshida S, Hiraga K, Takehana T, Taniguchi I, Yamaji H, Maeda Y, et al. A bacterium that degrades and assimilates poly(ethylene terephthalate). Science. 2016;351:1196-9 pubmed publisher..Both enzymes are required to enzymatically convert PET efficiently into its two environmentally benign monomers, terephthalic acid and ethylene glycol. ..
- Koshida S, Hirai Y. Identification of cellular recognition sequence of epimorphin and critical role of cell/epimorphin interaction in lung branching morphogenesis. Biochem Biophys Res Commun. 1997;234:522-5 pubmed..These results not only revealed a part of the functional mechanism of epimorphin but also demonstrated that cell/ epimorphin interaction through the NL-peptide sequence is a critical step for lung epithelial morphogenesis. ..
- Feniouk B, Suzuki T, Yoshida M. The role of subunit epsilon in the catalysis and regulation of FOF1-ATP synthase. Biochim Biophys Acta. 2006;1757:326-38 pubmed..Multiple functions of subunit epsilon, its role in the difference between the catalytic pathways of ATP synthesis and hydrolysis and its influence on the inhibition of ATP hydrolysis by ADP are also discussed. ..
- Shimada H, Mochizuki M, Ogura K, Froehlich J, Osteryoung K, Shirano Y, et al. Arabidopsis cotyledon-specific chloroplast biogenesis factor CYO1 is a protein disulfide isomerase. Plant Cell. 2007;19:3157-69 pubmed..These results suggest that CYO1 has a chaperone-like activity required for thylakoid biogenesis in cotyledons...
- Kawaguchi J, Takeshita S, Kashima T, Imai T, Machinami R, Kudo A. Expression and function of the splice variant of the human cadherin-11 gene in subordination to intact cadherin-11. J Bone Miner Res. 1999;14:764-75 pubmed..These findings suggest that expression of the variant form of human cadherin-11 may regulate the intact cadherin-11-mediated adhesion and alter the morphogenetic processes during mesenchymal cell differentiation including osteoblasts. ..
- Matsuo T, Ikeda A, Seki H, Ichimata T, Sugimori D, Nakamura S. Cloning and expression of the ferredoxin gene from extremely halophilic archaeon Haloarculajaponica strain TR-1. Biometals. 2001;14:135-42 pubmed..japonica host cells. The absorption and ESR spectra of the Fd/His Tag fusion protein revealed the presence of a [2Fe-2S] cluster which is characteristic of native Ha. japonica Fd...
- Tsuchiya T, Suzuki T, Yamada T, Shimada H, Masuda T, Ohta H, et al. Chlorophyllase as a serine hydrolase: identification of a putative catalytic triad. Plant Cell Physiol. 2003;44:96-101 pubmed..These results indicate that Chlase is a serine hydrolase and, by analogy with a plausible catalytic mechanism of serine hydrolases, we proposed a mechanism for hydrolysis catalyzed by Chlase...
- Miyazaki Y, Jojima T, Ono T, Yamazaki T, Shishido K. A cDNA homologue of Schizosaccharomyces pombe cdc5(+) from the mushroom Lentinula edodes: characterization of the cDNA and its expressed product. Biochim Biophys Acta. 2004;1680:93-102 pubmed..cdc5 gene is most actively transcribed in primordia and small immature fruiting bodies of L. edodes, implying that Le.cdc5 may play a role in the beginning and early stage of fruiting-body formation. ..
- Ogiso H, Kagi N, Matsumoto E, Nishimoto M, Arai R, Shirouzu M, et al. Phosphorylation analysis of 90 kDa heat shock protein within the cytosolic arylhydrocarbon receptor complex. Biochemistry. 2004;43:15510-9 pubmed..These results suggest that the phosphorylations in the charged linker region of the HSP90 molecule modulate the formation of the functional cytosolic AhR complex. ..
- Shintomi K, Iwabuchi M, Saeki H, Ura K, Kishimoto T, Ohsumi K. Nucleosome assembly protein-1 is a linker histone chaperone in Xenopus eggs. Proc Natl Acad Sci U S A. 2005;102:8210-5 pubmed..These results strongly suggest that NAP-1 functions as a chaperone for the linker histone in Xenopus eggs. ..
- Mochida K, Yoshida T, Sakurai T, Ogihara Y, Shinozaki K. TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics. Plant Physiol. 2009;150:1135-46 pubmed publisher..This informative content provides an informatics gateway for Triticeae genomics and grass comparative genomics. TriFLDB is publicly available at http://TriFLDB.psc.riken.jp/. ..
- Kim S, Nishihara R, Citterio D, Suzuki K. Genetically Encoded Molecular Tension Probe for Tracing Protein-Protein Interactions in Mammalian Cells. Bioconjug Chem. 2016;27:354-62 pubmed publisher..This study expands capabilities of luciferases as a tool for analyses of molecular dynamics and cell signaling in living subjects. ..