Experts and Doctors on tertiary protein structure in Suita, Ōsaka, Japan

Summary

Locale: Suita, Ōsaka, Japan
Topic: tertiary protein structure

Top Publications

  1. Saito T, Okuzaki D, Nojima H. Mcp5, a meiotic cell cortex protein, is required for nuclear movement mediated by dynein and microtubules in fission yeast. J Cell Biol. 2006;173:27-33 pubmed
    ..Our results suggest that Mcp5 localizes at the cell cortex through its PH domain and functions as a dynein anchor, thereby facilitating nuclear oscillation. ..
  2. Watari A, Yutsudo M. Multi-functional gene ASY/Nogo/RTN-X/RTN4: apoptosis, tumor suppression, and inhibition of neuronal regeneration. Apoptosis. 2003;8:5-9 pubmed
    ..Therefore, the products of this gene may be multi-functional, regulating apoptosis, tumor development, and neuronal regeneration. ..
  3. Nishiuchi R, Murayama O, Fujiwara H, Gu J, Kawakami T, Aimoto S, et al. Characterization of the ligand-binding specificities of integrin alpha3beta1 and alpha6beta1 using a panel of purified laminin isoforms containing distinct alpha chains. J Biochem. 2003;134:497-504 pubmed
  4. Nakagawa A, Miyazaki N, Taka J, Naitow H, Ogawa A, Fujimoto Z, et al. The atomic structure of rice dwarf virus reveals the self-assembly mechanism of component proteins. Structure. 2003;11:1227-38 pubmed
    ..These interactions suggest how the 900 protein components are built into a higher-ordered virus core structure. ..
  5. Shiraki T, Kodama T, Jingami H, Kamiya N. Rational discovery of a novel interface for a coactivator in the peroxisome proliferator-activated receptor gamma: theoretical implications of impairment in type 2 diabetes mellitus. Proteins. 2005;58:418-25 pubmed
    ..Thus, our model provides structural insight into the impairment of PPARgamma function in type 2 diabetes mellitus. ..
  6. Shimizu T, Yamanaka Y, Nojima H, Yabe T, Hibi M, Hirano T. A novel repressor-type homeobox gene, ved, is involved in dharma/bozozok-mediated dorsal organizer formation in zebrafish. Mech Dev. 2002;118:125-38 pubmed
    ..These results suggest that ved is a target for the repressor Dha/Boz. Ved functions redundantly with vox/vega1 and vent/vega2 to restrict the organizer domain. ..
  7. Shionyu Mitsuyama C, Ito Y, Konno A, Miwa Y, Ogawa T, Muramoto K, et al. In vitro evolutionary thermostabilization of congerin II: a limited reproduction of natural protein evolution by artificial selection pressure. J Mol Biol. 2005;347:385-97 pubmed
    ..The results showed that the artificial pressure made congerin II partially reproduce the natural evolution of congerin I...
  8. Fujimoto Y, Shiraki T, Horiuchi Y, Waku T, Shigenaga A, Otaka A, et al. Proline cis/trans-isomerase Pin1 regulates peroxisome proliferator-activated receptor gamma activity through the direct binding to the activation function-1 domain. J Biol Chem. 2010;285:3126-32 pubmed publisher
    ..Thus, our results suggest that Pin1 regulates macrophage function through the direct binding to the phosphorylated AF-1 domain of PPARgamma. ..
  9. Okamura Y, Murata Y, Iwasaki H. Voltage-sensing phosphatase: actions and potentials. J Physiol. 2009;587:513-20 pubmed publisher
    ..The recent discovery of a voltage-sensing phosphatase, VSP, has changed the idea that voltage sensors are unique to ion flux through membranes. Recent findings on mechanisms and potential applications of VSP are reviewed. ..

More Information

Publications87

  1. Yagi H, Kajiwara N, Iwabuchi T, Izumi K, Yoshida M, Akutsu H. Stepwise propagation of the ATP-induced conformational change of the F1-ATPase beta subunit revealed by NMR. J Biol Chem. 2009;284:2374-82 pubmed publisher
    ..Actually, MgATP induced a conformational change around Tyr-307 (311 for MF1beta), whereas MgADP did not. The significance of these findings is discussed in connection with the catalytic rotation of F1-ATPase. ..
  2. Minamino T, Shimada M, Okabe M, Saijo Hamano Y, Imada K, Kihara M, et al. Role of the C-terminal cytoplasmic domain of FlhA in bacterial flagellar type III protein export. J Bacteriol. 2010;192:1929-36 pubmed publisher
  3. Kametaka A, Takagi M, Hayakawa T, Haraguchi T, Hiraoka Y, Yoneda Y. Interaction of the chromatin compaction-inducing domain (LR domain) of Ki-67 antigen with HP1 proteins. Genes Cells. 2002;7:1231-42 pubmed
    ..Marsupial chmadrin and human pKi-67 induce chromatin compaction across species, possibly via the interaction of its LR domain with HP1. ..
  4. Nagano F, Kawabe H, Nakanishi H, Shinohara M, Deguchi Tawarada M, Takeuchi M, et al. Rabconnectin-3, a novel protein that binds both GDP/GTP exchange protein and GTPase-activating protein for Rab3 small G protein family. J Biol Chem. 2002;277:9629-32 pubmed
    ..These results indicate that rabconnectin-3 serves as a scaffold molecule for both Rab3 GEP and GAP on synaptic vesicles. ..
  5. Morita T, Mayanagi T, Sobue K. Dual roles of myocardin-related transcription factors in epithelial mesenchymal transition via slug induction and actin remodeling. J Cell Biol. 2007;179:1027-42 pubmed
    ..MRTFs also increase the expression levels of actin cytoskeletal proteins via serum response factor, thereby triggering reorganization of the actin cytoskeleton. Thus, MRTFs are important mediators of TGF-beta1-induced EMT. ..
  6. Nagashima K, Endo A, Ogita H, Kawana A, Yamagishi A, Kitabatake A, et al. Adaptor protein Crk is required for ephrin-B1-induced membrane ruffling and focal complex assembly of human aortic endothelial cells. Mol Biol Cell. 2002;13:4231-42 pubmed
    ..These results indicated that Crk plays a critical role in Rac1-induced membrane ruffling and Rap1-mediated nascent focal complex stabilization contributing to ephrin-B1-induced human aortic endothelial cells migration. ..
  7. Tanaka H, Kato K, Yamashita E, Sumizawa T, Zhou Y, Yao M, et al. The structure of rat liver vault at 3.5 angstrom resolution. Science. 2009;323:384-8 pubmed publisher
    ..Interactions between the 42-turn-long cap-helix domains are key to stabilizing the particle. The shoulder domain is structurally similar to a core domain of stomatin, a lipid-raft component in erythrocytes and epithelial cells...
  8. Takano A, HOE H, Isojima Y, Nagai K. Analysis of the expression, localization and activity of rat casein kinase 1epsilon-3. Neuroreport. 2004;15:1461-4 pubmed
    ..Moreover, the kinase activity of the rCK1epsilon-3 protein differed from that of rCK1epsilon-1. These data suggest that rCK1epsilon-1 and rCK1epsilon-3 may play different functional roles. ..
  9. Ishikawa M, Tsuchiya D, Oyama T, Tsunaka Y, Morikawa K. Structural basis for channelling mechanism of a fatty acid beta-oxidation multienzyme complex. EMBO J. 2004;23:2745-54 pubmed
    ..This channelling mechanism could be applied to other beta-oxidation multienzymes, as revealed from the homology model of the human mitochondrial trifunctional enzyme complex. ..
  10. Wakamatsu T, Kitamura Y, Kotera Y, Nakagawa N, Kuramitsu S, Masui R. Structure of RecJ exonuclease defines its specificity for single-stranded DNA. J Biol Chem. 2010;285:9762-9 pubmed publisher
    ..In addition, the structure of the RecJ-Mn(2+) complex suggests that the hydrolysis reaction catalyzed by RecJ proceeds through a two-metal ion mechanism...
  11. Takano K, Tsuchimori K, Yamagata Y, Yutani K. Effect of foreign N-terminal residues on the conformational stability of human lysozyme. Eur J Biochem. 1999;266:675-82 pubmed
  12. Saito T, Miyoshi E, Sasai K, Nakano N, Eguchi H, Honke K, et al. A secreted type of beta 1,6-N-acetylglucosaminyltransferase V (GnT-V) induces tumor angiogenesis without mediation of glycosylation: a novel function of GnT-V distinct from the original glycosyltransferase activity. J Biol Chem. 2002;277:17002-8 pubmed
    ..These findings provide some novel information on the relationship between GnT-V and tumor metastasis. The inhibition of GnT-V secretion or its expression represents a novel potential strategy for the inhibition of tumor angiogenesis. ..
  13. Shinohara M, Sato N, Kurinami H, Takeuchi D, Takeda S, Shimamura M, et al. Reduction of brain beta-amyloid (Abeta) by fluvastatin, a hydroxymethylglutaryl-CoA reductase inhibitor, through increase in degradation of amyloid precursor protein C-terminal fragments (APP-CTFs) and Abeta clearance. J Biol Chem. 2010;285:22091-102 pubmed publisher
    ..These results have important implications for the development of disease-modifying therapy for Alzheimer disease as well as understanding of Abeta metabolism. ..
  14. Sakumoto N, Yamashita H, Mukai Y, Kaneko Y, Harashima S. Dual-specificity protein phosphatase Yvh1p, which is required for vegetative growth and sporulation, interacts with yeast pescadillo homolog in Saccharomyces cerevisiae. Biochem Biophys Res Commun. 2001;289:608-15 pubmed
    ..These observations indicate that Yph1p plays a role in sporulation in addition to cell cycle progression, and is a candidate for a substrate or a regulatory subunit of Yvh1p. ..
  15. Kohbushi H, Nakai Y, Kikuchi S, Yabe T, Hori H, Nakai M. Arabidopsis cytosolic Nbp35 homodimer can assemble both [2Fe-2S] and [4Fe-4S] clusters in two distinct domains. Biochem Biophys Res Commun. 2009;378:810-5 pubmed publisher
    ..Taken together, our data suggest that Nbp35 plays a pivotal role in iron-sulfur cluster assembly and delivery in the plant cell cytosol as a bifunctional molecular scaffold. ..
  16. Toyofuku T, Zhang H, Kumanogoh A, Takegahara N, Yabuki M, Harada K, et al. Guidance of myocardial patterning in cardiac development by Sema6D reverse signalling. Nat Cell Biol. 2004;6:1204-11 pubmed
    ..Thus, Sema6D coordinates both compact-layer expansion and trabeculation, functioning as both a ligand and a receptor for Plexin-A1. ..
  17. Kametaka S, Shibata M, Moroe K, Kanamori S, Ohsawa Y, Waguri S, et al. Identification of phospholipid scramblase 1 as a novel interacting molecule with beta -secretase (beta -site amyloid precursor protein (APP) cleaving enzyme (BACE)). J Biol Chem. 2003;278:15239-45 pubmed
    ..Taken together, our current study suggests the functional involvement of PLSCR1 in the intracellular distribution of BACE and/or recruitment of BACE into the detergent-insoluble lipid raft. ..
  18. Yabe T, Yamashita E, Kikuchi A, Morimoto K, Nakagawa A, Tsukihara T, et al. Structural analysis of Arabidopsis CnfU protein: an iron-sulfur cluster biosynthetic scaffold in chloroplasts. J Mol Biol. 2008;381:160-73 pubmed publisher
    ..We propose that such a structural framework is important for CnfU to function as a Fe-S cluster biosynthetic scaffold. ..
  19. Sakurai A, Fukuhara S, Yamagishi A, Sako K, Kamioka Y, Masuda M, et al. MAGI-1 is required for Rap1 activation upon cell-cell contact and for enhancement of vascular endothelial cadherin-mediated cell adhesion. Mol Biol Cell. 2006;17:966-76 pubmed
    ..In addition, once activated, Rap1 upon cell-cell contacts positively regulate the adherens junction formation by relocating vinculin that supports VE-cadherin-based cell adhesion. ..
  20. Xie Y, Inoue T, Seike N, Matsumura H, Kanbayashi K, Itoh K, et al. Crystallization and preliminary X-ray crystallographic studies of dissimilatory nitrite reductase isolated from Hyphomicrobium denitrificans A3151. Acta Crystallogr D Biol Crystallogr. 2004;60:2383-6 pubmed
    ..X-ray diffraction data were collected to 3.5 A resolution. To solve the crystal structure of HdNIR, the multiwavelength anomalous dispersion (MAD) method and the molecular-replacement method are currently being used...
  21. Toma S, Chong K, Nakagawa A, Teranishi K, Inouye S, Shimomura O. The crystal structures of semi-synthetic aequorins. Protein Sci. 2005;14:409-16 pubmed
    ..The differences of various semi-synthetic aequorins in Ca(2+)-sensitivity and reaction rate are explained by the capability of the involved groups and structures to undergo conformational changes in response to the Ca(2+)-binding...
  22. Nishimura M, Yoshida T, Shirouzu M, Terada T, Kuramitsu S, Yokoyama S, et al. Solution structure of ribosomal protein L16 from Thermus thermophilus HB8. J Mol Biol. 2004;344:1369-83 pubmed
    ..This suggests the direct participation of L16 as a part of the binding site for antibiotics. ..
  23. Yagi H, Kajiwara N, Tanaka H, Tsukihara T, Kato Yamada Y, Yoshida M, et al. Structures of the thermophilic F1-ATPase epsilon subunit suggesting ATP-regulated arm motion of its C-terminal domain in F1. Proc Natl Acad Sci U S A. 2007;104:11233-8 pubmed publisher
    ..These results suggest that the epsilon C-terminal domain can undergo an arm-like motion in response to an ATP concentration change and thereby contribute to regulation of F(o)F(1)-ATP synthase...
  24. Tsuji N, Nishikori S, Iwabe O, Matsumoto S, Shiraki K, Miyasaka H, et al. Comparative analysis of the two-step reaction catalyzed by prokaryotic and eukaryotic phytochelatin synthase by an ion-pair liquid chromatography assay. Planta. 2005;222:181-91 pubmed
    ..These results enable us to propose an advanced model of PC synthesis, describing substrate specificity, heavy metal requirement, and the active site in the enzyme. ..
  25. Takinowaki H, Matsuda Y, Yoshida T, Kobayashi Y, Ohkubo T. The solution structure of the methylated form of the N-terminal 16-kDa domain of Escherichia coli Ada protein. Protein Sci. 2006;15:487-97 pubmed
    ..Thus, after the Cys38 methylation, the MTase subdomain can bind the cognate DNA because the negative charge of the zinc-thiolate center is reduced. ..
  26. Yamamoto M, Takeda K, Akira S. TIR domain-containing adaptors define the specificity of TLR signaling. Mol Immunol. 2004;40:861-8 pubmed
    ..Indeed, two additional TIR domain-containing adaptors, TIRAP/Mal and TRIF, have recently been identified. Both define the specific biological responses of each TLR. ..
  27. Tokuoka K, Kusakari Y, Krungkrai S, Matsumura H, Kai Y, Krungkrai J, et al. Structural basis for the decarboxylation of orotidine 5'-monophosphate (OMP) by Plasmodium falciparum OMP decarboxylase. J Biochem. 2008;143:69-78 pubmed
    ..The structural basis of substrate or product binding to PfOMPDC will help to uncover the decarboxylation mechanism and facilitate structure-based optimization of antimalarial drugs. ..
  28. Nakaishi A, Hirose M, Yoshimura M, Oneyama C, Saito K, Kuki N, et al. Structural insight into the specific interaction between murine SHPS-1/SIRP alpha and its ligand CD47. J Mol Biol. 2008;375:650-60 pubmed
  29. Kogata N, Masuda M, Kamioka Y, Yamagishi A, Endo A, Okada M, et al. Identification of Fer tyrosine kinase localized on microtubules as a platelet endothelial cell adhesion molecule-1 phosphorylating kinase in vascular endothelial cells. Mol Biol Cell. 2003;14:3553-64 pubmed
    ..These results suggest that Fer localized on microtubules may play an important role in phosphorylation of PECAM-1, possibly through its association with p120catenin at nascent cell-cell contacts. ..
  30. Foophow T, Tanaka S, Angkawidjaja C, Koga Y, Takano K, Kanaya S. Crystal structure of a subtilisin homologue, Tk-SP, from Thermococcus kodakaraensis: requirement of a C-terminal beta-jelly roll domain for hyperstability. J Mol Biol. 2010;400:865-77 pubmed publisher
    ..We propose that attachment of a beta-jelly roll domain to the C-terminus is one of the strategies of the proteins from hyperthermophiles to adapt to high-temperature environment...
  31. Yin T, Maekawa K, Kamide K, Saito Y, Hanada H, Miyashita K, et al. Genetic variations of CYP2C9 in 724 Japanese individuals and their impact on the antihypertensive effects of losartan. Hypertens Res. 2008;31:1549-57 pubmed publisher
    ..CYP2C9*30 might be associated with a diminished response to the antihypertensive effects of losartan. ..
  32. Shoji Kawata S, Zhong Q, Kameoka M, Iwabu Y, Sapsutthipas S, Luftig R, et al. The RING finger ubiquitin ligase RNF125/TRAC-1 down-modulates HIV-1 replication in primary human peripheral blood mononuclear cells. Virology. 2007;368:191-204 pubmed
    ..These results suggest that RNF125/TRAC-1 could function to recruit host factor(s) controlling HIV-1 transcription to the ubiquitin-proteasome pathway. ..
  33. Horike N, Takemori H, Katoh Y, Doi J, Min L, Asano T, et al. Adipose-specific expression, phosphorylation of Ser794 in insulin receptor substrate-1, and activation in diabetic animals of salt-inducible kinase-2. J Biol Chem. 2003;278:18440-7 pubmed
  34. Yamada K, Miyata T, Tsuchiya D, Oyama T, Fujiwara Y, Ohnishi T, et al. Crystal structure of the RuvA-RuvB complex: a structural basis for the Holliday junction migrating motor machinery. Mol Cell. 2002;10:671-81 pubmed
  35. Tanaka S, Saito K, Chon H, Matsumura H, Koga Y, Takano K, et al. Crystal structure of unautoprocessed precursor of subtilisin from a hyperthermophilic archaeon: evidence for Ca2+-induced folding. J Biol Chem. 2007;282:8246-55 pubmed publisher
  36. Kamakura A, Fujimoto Y, Motohashi Y, Ohashi K, Ohashi Kobayashi A, Maeda M. Functional dissection of transmembrane domains of human TAP-like (ABCB9). Biochem Biophys Res Commun. 2008;377:847-51 pubmed publisher
    ..These results suggest that the sorting signal for lysosomes is present within the amino-terminal transmembrane domain (Met(1)-Arg(141)) of the TAPL molecule...
  37. Sumi T, Matsumoto K, Nakamura T. Specific activation of LIM kinase 2 via phosphorylation of threonine 505 by ROCK, a Rho-dependent protein kinase. J Biol Chem. 2001;276:670-6 pubmed
    ..Together with the finding that LIMK1 is regulated by Pak1, LIMK1 and LIMK2 are regulated by different protein kinases downstream of distinct Rho family GTPases. ..
  38. Nishida T, Kanda T, Nishitani A, Takahashi T, Nakajima K, Ishikawa T, et al. Secondary mutations in the kinase domain of the KIT gene are predominant in imatinib-resistant gastrointestinal stromal tumor. Cancer Sci. 2008;99:799-804 pubmed publisher
    ..Resistant lesions showed monoclonal development of tumor cells. Taken together, additional cis-positioned mutations in the kinase domains are a major cause of secondary resistance to imatinib in Japanese GIST patients. ..
  39. Egawa A, Fujiwara T, Mizoguchi T, Kakitani Y, Koyama Y, Akutsu H. Structure of the light-harvesting bacteriochlorophyll c assembly in chlorosomes from Chlorobium limicola determined by solid-state NMR. Proc Natl Acad Sci U S A. 2007;104:790-5 pubmed
    ..This work constitutes an important advance in the structure determination of huge intact systems that cannot be crystallized...
  40. Bando S, Takano T, Yubisui T, Shirabe K, Takeshita M, Nakagawa A. Structure of human erythrocyte NADH-cytochrome b5 reductase. Acta Crystallogr D Biol Crystallogr. 2004;60:1929-34 pubmed
    ..The structures around 15 mutation sites of the human reductase have been examined for the influence of residue substitutions using the program ROTAMER. Five mutations in the FAD-binding domain seem to be related to cytochrome b(5). ..
  41. Yamada M, Suzuki K, Mizutani M, Asada A, Matozaki T, Ikeuchi T, et al. Analysis of tyrosine phosphorylation-dependent protein-protein interactions in TrkB-mediated intracellular signaling using modified yeast two-hybrid system. J Biochem. 2001;130:157-65 pubmed
    ..Therefore, we show that the two-and-a-half-hybrid system is a powerful tool for studying tyrosine phosphorylation-dependent protein-protein interactions in intracellular signaling pathways stimulated by TrkB receptor tyrosine kinase. ..
  42. Hotta K, Funahashi T, Matsukawa Y, Takahashi M, Nishizawa H, Kishida K, et al. Galectin-12, an Adipose-expressed Galectin-like Molecule Possessing Apoptosis-inducing Activity. J Biol Chem. 2001;276:34089-97 pubmed
    ..These results suggest that galectin-12, an adipose-expressed galectin-like molecule, may participate in the apoptosis of adipocytes. ..
  43. Yang J, Kamide K, Kokubo Y, Takiuchi S, Tanaka C, Banno M, et al. Genetic variations of regulator of G-protein signaling 2 in hypertensive patients and in the general population. J Hypertens. 2005;23:1497-505 pubmed
    ..47; 95% CI 1.09-1.97; P = 0.012), with hypertension in women by multivariate logistic regression analysis. Our results suggest that genetic variations in RGS2 contribute partly to the hypertensive phenotype. ..
  44. Watanabe D, Saijoh Y, Nonaka S, Sasaki G, Ikawa Y, Yokoyama T, et al. The left-right determinant Inversin is a component of node monocilia and other 9+0 cilia. Development. 2003;130:1725-34 pubmed
    ..These results suggest that the Inv protein contributes to left-right determination as a component of monocilia in the node and is essential for the generation of normal nodal flow. ..
  45. Kanamoto T, Terada K, Yoshikawa H, Furukawa T. Cloning and expression pattern of lbx3, a novel chick homeobox gene. Gene Expr Patterns. 2006;6:241-6 pubmed
    ..In addition, lbx3 transcripts are detected in the medial dermomyotomal lips of somites of all axial levels at stage 23, but not detected in the neural tube. ..
  46. Nishikawa S, Arimoto I, Ikezaki K, Sugawa M, Ueno H, Komori T, et al. Switch between large hand-over-hand and small inchworm-like steps in myosin VI. Cell. 2010;142:879-88 pubmed publisher
    ..Switching between these two mechanisms in a strain-sensitive, ADP-dependent manner allows myosin VI to fulfill its multiple cellular tasks including vesicle transport and membrane anchoring. ..
  47. Kakunaga S, Ikeda W, Itoh S, Deguchi Tawarada M, Ohtsuka T, Mizoguchi A, et al. Nectin-like molecule-1/TSLL1/SynCAM3: a neural tissue-specific immunoglobulin-like cell-cell adhesion molecule localizing at non-junctional contact sites of presynaptic nerve terminals, axons and glia cell processes. J Cell Sci. 2005;118:1267-77 pubmed
  48. Sato S, Sugiyama M, Yamamoto M, Watanabe Y, Kawai T, Takeda K, et al. Toll/IL-1 receptor domain-containing adaptor inducing IFN-beta (TRIF) associates with TNF receptor-associated factor 6 and TANK-binding kinase 1, and activates two distinct transcription factors, NF-kappa B and IFN-regulatory factor-3, in the Toll-li. J Immunol. 2003;171:4304-10 pubmed
    ..Taken together, these results demonstrate that TRIF associates with TRAF6 and TBK1 independently, and activates two distinct transcription factors, NF-kappaB and IFN regulatory factor-3, respectively. ..
  49. Waku T, Shiraki T, Oyama T, Fujimoto Y, Maebara K, Kamiya N, et al. Structural insight into PPARgamma activation through covalent modification with endogenous fatty acids. J Mol Biol. 2009;385:188-99 pubmed publisher
    ..This study presents the structural basis for the activation and modulation mechanism of PPARgamma through covalent modification with endogenous fatty acids. ..
  50. Kishima Y, Yamamoto H, Izumoto Y, Yoshida K, Enomoto H, Yamamoto M, et al. Hepatoma-derived growth factor stimulates cell growth after translocation to the nucleus by nuclear localization signals. J Biol Chem. 2002;277:10315-22 pubmed
    ..These findings suggest that the gene-specific region, at least the bipartite NLS sequence and the N- and C-terminal neighboring portions, is essential for the mitogenic activity of HDGF after nuclear translocation. ..
  51. Angkawidjaja C, Matsumura H, Koga Y, Takano K, Kanaya S. X-ray crystallographic and MD simulation studies on the mechanism of interfacial activation of a family I.3 lipase with two lids. J Mol Biol. 2010;400:82-95 pubmed publisher
    ..These results suggest that Ca1 functions as a hook for stabilization of a fully opened conformation of lid1 and for initiation of subsequent opening of lid2. ..
  52. Nomura R, Suzuki Y, Kakizuka A, Jingami H. Direct detection of the interaction between recombinant soluble extracellular regions in the heterodimeric metabotropic gamma-aminobutyric acid receptor. J Biol Chem. 2008;283:4665-73 pubmed publisher
    ..These results not only open the way to future structural studies but also highlight the role of the interaction between the extracellular regions, which controls agonist affinity to the heterodimeric receptor. ..
  53. Nada S, Shima T, Yanai H, Husi H, Grant S, Okada M, et al. Identification of PSD-93 as a substrate for the Src family tyrosine kinase Fyn. J Biol Chem. 2003;278:47610-21 pubmed
    ..These results suggest that PSD-93 serves as a membrane-anchored substrate of Fyn and plays a role in the regulation of Fyn-mediated modification of NMDA receptor function. ..
  54. Inoue T, Suzuki S, Nishio N, Yamaguchi K, Kataoka K, Tobari J, et al. The significance of the flexible loop in the azurin (Az-iso2) from the obligate methylotroph Methylomonas sp. strain J. J Mol Biol. 2003;333:117-24 pubmed
    ..We discuss why the electron-transfer activity of Az-iso2 is fivefold higher than that of Az-iso1...
  55. Matsuoka H, Nada S, Okada M. Mechanism of Csk-mediated down-regulation of Src family tyrosine kinases in epidermal growth factor signaling. J Biol Chem. 2004;279:5975-83 pubmed
  56. Tanaka H, Iguchi N, Isotani A, Kitamura K, Toyama Y, Matsuoka Y, et al. HANP1/H1T2, a novel histone H1-like protein involved in nuclear formation and sperm fertility. Mol Cell Biol. 2005;25:7107-19 pubmed
    ..I. Martianov, S. Brancorsini, R. Catena, A. Gansmuller, N. Kotaja, M. Parvinen, P. Sassone-Corsi, and I. Davidson, Proc. Natl. Acad. Sci. USA 102:2808-2813, 2005) that reported similar results. ..
  57. Yamamoto T, Matsuda T, Inoue T, Matsumura H, Morikawa M, Kanaya S, et al. Crystal structure of TBP-interacting protein (Tk-TIP26) and implications for its inhibition mechanism of the interaction between TBP and TATA-DNA. Protein Sci. 2006;15:152-61 pubmed publisher
  58. Sadik G, Tanaka T, Kato K, Yanagi K, Kudo T, Takeda M. Differential interaction and aggregation of 3-repeat and 4-repeat tau isoforms with 14-3-3zeta protein. Biochem Biophys Res Commun. 2009;383:37-41 pubmed publisher
    ..The significant aggregation of 4R-tau by 14-3-3zeta suggests that 14-3-3 may act as an inducer in the generation of 4R-tau-predominant neurofibrillary tangles in tauopathies. ..
  59. Nogi T, Yasui N, Mihara E, Matsunaga Y, Noda M, Yamashita N, et al. Structural basis for semaphorin signalling through the plexin receptor. Nature. 2010;467:1123-7 pubmed publisher
  60. Banno F, Chauhan A, Kokame K, Yang J, Miyata S, Wagner D, et al. The distal carboxyl-terminal domains of ADAMTS13 are required for regulation of in vivo thrombus formation. Blood. 2009;113:5323-9 pubmed publisher
    ..These results suggested that the C-terminally truncated ADAMTS13 exhibited decreased activity in the cleavage of VWF under high shear rate. Role of the C-terminal domains may become increasingly important under prothrombotic conditions. ..
  61. Taniguchi Y, Ido H, Sanzen N, Hayashi M, Sato Nishiuchi R, Futaki S, et al. The C-terminal region of laminin beta chains modulates the integrin binding affinities of laminins. J Biol Chem. 2009;284:7820-31 pubmed publisher
    ..Taken together, the results provide evidence that the C-terminal region of beta chains is involved in laminin recognition by integrins and modulates the binding affinities of laminins toward X2-type integrins. ..
  62. Yamagishi A, Masuda M, Ohki T, Onishi H, Mochizuki N. A novel actin bundling/filopodium-forming domain conserved in insulin receptor tyrosine kinase substrate p53 and missing in metastasis protein. J Biol Chem. 2004;279:14929-36 pubmed
    ..Our results indicate that IRSp53, when activated by small GTPases, participates in F-actin reorganization not only in an SH3-dependent manner but also in a manner dependent on the activity of the IMD. ..
  63. Kihara M, Nakai W, Asano S, Suzuki A, Kitada K, Kawasaki Y, et al. Characterization of the yeast Cdc7p/Dbf4p complex purified from insect cells. Its protein kinase activity is regulated by Rad53p. J Biol Chem. 2000;275:35051-62 pubmed
    ..This result suggests that Rad53p controls the initiation of chromosomal DNA replication by regulating the protein kinase activity associated with the Cdc7p/Dbf4p complex. ..
  64. Kamachi Y, Uchikawa M, Tanouchi A, Sekido R, Kondoh H. Pax6 and SOX2 form a co-DNA-binding partner complex that regulates initiation of lens development. Genes Dev. 2001;15:1272-86 pubmed
  65. Hong D, Hagihara Y, Kato H, Goto Y. Flexible loop of beta 2-glycoprotein I domain V specifically interacts with hydrophobic ligands. Biochemistry. 2001;40:8092-100 pubmed
    ..These results suggested that the interaction of Domain V with hydrophobic compounds through the flexible loop is similar to the binding of hydrophobic compounds to the protein folding intermediate. ..
  66. Liu L, Komori K, Ishino S, Bocquier A, Cann I, Kohda D, et al. The archaeal DNA primase: biochemical characterization of the p41-p46 complex from Pyrococcus furiosus. J Biol Chem. 2001;276:45484-90 pubmed
    ..furiosus, in a similar fashion to the eukaryotic polymerase alpha-primase complex. ..
  67. Su X, Pang T, Wakabayashi S, Shigekawa M. Evidence for involvement of the putative first extracellular loop in differential volume sensitivity of the Na+/H+ exchangers NHE1 and NHE2. Biochemistry. 2003;42:1086-94 pubmed
    ..The data suggest that the putative first extracellular loop of NHE2, but not that of NHE1, may exert an inhibitory influence on hyperosmolarity-induced activation of the exchanger and thereby block RVI. ..
  68. Sasai K, Ikeda Y, Ihara H, Honke K, Taniguchi N. Caveolin-1 regulates the functional localization of N-acetylglucosaminyltransferase III within the golgi apparatus. J Biol Chem. 2003;278:25295-301 pubmed
    ..Caveolin-1 may modify the biosynthetic pathway of sugar chains via the regulation of the intra-Golgi subcompartment localization of this key glycosyltransferase. ..
  69. Yamashita Y, Miura R, Takemoto Y, Tsuda S, Kawahara H, Obata H. Type II antifreeze protein from a mid-latitude freshwater fish, Japanese smelt (Hypomesus nipponensis). Biosci Biotechnol Biochem. 2003;67:461-6 pubmed
    ..0% identical with the entire herring AFP gene. The cDNA and amino acid sequence of the Japanese smelt AFP were the same length as those of herring AFP...
  70. Iwata K, Fujiwara T, Matsuki Y, Akutsu H, Takahashi S, Naiki H, et al. 3D structure of amyloid protofilaments of beta2-microglobulin fragment probed by solid-state NMR. Proc Natl Acad Sci U S A. 2006;103:18119-24 pubmed
    ..By revealing the structure of beta(2)-microglobulin protofilament-like fibrils, this work represents technical progress in analyzing amyloid fibrils in general through solid-state NMR. ..
  71. Tanaka S, Matsumura H, Koga Y, Takano K, Kanaya S. Four new crystal structures of Tk-subtilisin in unautoprocessed, autoprocessed and mature forms: insight into structural changes during maturation. J Mol Biol. 2007;372:1055-69 pubmed publisher
    ..65 A resolution. This structure is virtually identical with that of the autoprocessed form, indicating that the interaction between the two domains is highly intensive and specific...
  72. Kojima S, Furukawa Y, Matsunami H, Minamino T, Namba K. Characterization of the periplasmic domain of MotB and implications for its role in the stator assembly of the bacterial flagellar motor. J Bacteriol. 2008;190:3314-22 pubmed publisher
    ..We propose that the MotB(C) dimer domain plays an important role in targeting and stable anchoring of the MotA/MotB complex to putative stator-binding sites of the motor. ..
  73. Lee Y, Chatani E, Sasahara K, Naiki H, Goto Y. A comprehensive model for packing and hydration for amyloid fibrils of beta2-microglobulin. J Biol Chem. 2009;284:2169-75 pubmed publisher
    ..These volumetric differences would result from the nature of main-chain-dominated fibrillogenesis. We suggest comprehensive models for these three types of fibrils illustrating packing and hydrational states. ..
  74. Nakayama E, Shioda T. Anti-retroviral activity of TRIM5 alpha. Rev Med Virol. 2010;20:77-92 pubmed publisher
    ..Accurate structural analysis of the binding surface between the viral capsid protein and TRIM5 alpha SPRY is thus required for the development of new antiretroviral drugs that enhance anti-HIV-1 activity of human TRIM5 alpha. ..
  75. Murakami M, Kamimura D, Hirano T. New IL-6 (gp130) family cytokine members, CLC/NNT1/BSF3 and IL-27. Growth Factors. 2004;22:75-7 pubmed
  76. Masuda M, Takeda S, Sone M, Ohki T, Mori H, Kamioka Y, et al. Endophilin BAR domain drives membrane curvature by two newly identified structure-based mechanisms. EMBO J. 2006;25:2889-97 pubmed
    ..We here propose that the BAR domain drives membrane curvature by coordinate action of the crescent's scaffold mechanism and the ridge's membrane insertion in addition to membrane binding via amino-terminal amphipathic helix. ..
  77. Yabuta N, Onda H, Watanabe M, Yoshioka N, Nagamori I, Funatsu T, et al. Isolation and characterization of the TIGA genes, whose transcripts are induced by growth arrest. Nucleic Acids Res. 2006;34:4878-92 pubmed
    ..Further analysis of the TIGA genes we have identified here may help us to better understand the mechanisms that regulate the G0 phase. ..
  78. Yasui N, Nogi T, Kitao T, Nakano Y, Hattori M, Takagi J. Structure of a receptor-binding fragment of reelin and mutational analysis reveal a recognition mechanism similar to endocytic receptors. Proc Natl Acad Sci U S A. 2007;104:9988-93 pubmed