分子夾雑の生命化学

menu

Original papers A02 Group

[すべて]　[A01の成果]　[A02の成果]　[A03の成果]　

  1. Takahashi. S.; A. Brazier. J.; Sugimoto. N., Topological impact of noncanonical DNA structures on Klenow fragment of DNA polymerase, Proc. Natl. Acad. Sci. U. S. A., 2017, 114, 9605-9610
    DOI: 10.1073/pnas.1704258114
    Tags: 杉本 A02
  2. Tateishi-Karimata. H.; Kawauchi. K.; Sugimoto. N.,Destabilization of DNA G-quadruplexes by chemical environment changes during tumor progression facilitates transcription, J. Am. Chem. Soc, 2018, 140 (2), pp 642–651
    DOI: 10.1021/jacs.7b09449
    Tags: 杉本 A02
  3. Teng. Y.; Pramanik. S.; Tateishi-Karimata H.; Ohyama. T.; Sugimoto. N., Drastic stability change of X-X mismatch in d(CXG) trinucleotide repeat disorders under molecular crowding condition, Biochem. Biophys. Res. Commun., 2018, 496, 2, 642-651, DOI: 10.1016/j.bbrc.2018.01.083. 
    Tags: 杉本A02

  4. Sakurai, K.; Yagi, M.; Konuma, T.; Takahashi, S.; Nishimura, C.; Goto, Y., Non-Native alpha-Helices in the Initial Folding Intermediate Facilitate the Ordered Assembly of the beta-Barrel in beta-Lactoglobulin, Biochemistry, 2017, 56 (36), 4799-4807. DOI: 10.1021/acs.biochem.7b00458
    Tags: 後藤 A02

  5. Matsushita, Y.; Sekiguchi, H.; Chang, J. W.; Nishijima, M.; Ikezaki, K.; Hamada, D.; Goto, Y.; Sasaki, Y.C., Nanoscale dynamics of protein assembly networks in supersaturated solutions, Scientific Reports, 2017, 7, 13883. DOI: 10.1038/s41598-017-14022-7
    Tags: 後藤 A02

  6. Nitani, A.; Muta, H.; Adachi, M.; So, M.; Sasahara, K.; Sakurai, K.; Chatani, E.; Naoe, K.; Ogi, H.; Hall, D.; Goto, Y., Heparin-dependent aggregation of hen egg white lysozyme reveals two distinct mechanisms of amyloid fibrillation, J. Biol. Chem., 2017, 292 (52), 21219-21230.
    DOI: 10.1074/jbc.M117.813097
    Tags: 後藤 A02

  7. Matsunaga, S.; Hano, Y.;  Saito, Y.; Fujimoto, K.J.; Kumasaka, T.; Matsumoto, S.; Kataoka, T.; Shima, F.; Tanaka, S., Structural Transition of Solvated H-Ras/GTP Revealed by Molecular Dynamics Simulation and Local Network Entropy, J. Mol. Graph. Model. 77 (2017) 51-63.
    DOI: 10.1016/j.jmgm.2017.07.028
    Tags: 田中 A02

  8. Tanaka, S., Information Geometrical Characterization of the Onsager-Machlup Process, Chem. Phys. Lett. 689 (2017) 152-155. 
    DOI: 10.1016/j.cplett.2017.10.005 
    Tags: 田中 A02

  9. Sato. N.; Takahashi. S.; Tateishi-Karimata. H.; Hazemi.E. M.; Chikuni. T.; Onizuka. K.; Sugimoto. N.,Alkylating Probes for G-Quadruplex Structure and Evaluation of the Properties of the Alkylated G-Quadruplex DNA Org. Biomol. Chem.,2018, 16,1436-1441 DOI:10.1039/C7OB03179C
    Tags: 杉本A02

  10. Natan. E.; Endoh. T.; Haim-Vilmovsky. L.; Flock. T.; Chalancon. G.; Hopper. J. T. S.; Kintses. B.; Horvath. P.; Daruka.L.; Fekete. G.; Pál. C.; Papp. B.; Oszi.E.; Magyar. Z.; Marsh. J.A.; Elcock. A.H.; Babu. M.N.; Robinson.C.V.; Sugimoto. N.; Teichmann. S.A., Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins, Nat Struct Mol Biol.,2018, 25, 279-288,
    DOI:10.1038/s41594-018-0029-5.
    Tags: 杉本A02
  11. Trajkovski, T, Endoh, H. Tateishi-Karimata, T. Ohyama, S. Tanaka, J. Plavec and N. Sugimoto, Pursuing origins of (poly)ethylene glycol-induced G-quadruplex structural modulations, Nucleic Acids Res., Accepted (2018)
    Tags: 杉本A02
  12. Usui. K.; Okada. A.; Sakashita. S.; Shimooka. M.; Tsuruoka. T.; Nakano. S.; Miyoshi. D.; Mashima. T.; Katahira. M.; Hamada. Y., DNA G-Wire Formation Using an Artificial Peptide is Controlled by Protease Activity, Molecules, 2017, 22, 1991
    Tags: 杉本 A02
  13. Teng. Y.; Pramanik. S.; Tateishi-Karimata H.; Ohyama. T.; Sugimoto. N., Drastic stability change of X-X mismatch in d(CXG) trinucleotide repeat disorders under molecular crowding condition, Biochem. Biophys. Res. Commun., 2018, 496, 2, 642-651, DOI: 10.1016/j.bbrc.2018.01.083.                                               
    Tags: 杉本A02
  14. Takahashi. S.; Kim T. K.; Podbevsek. P.; Plavec. J.; Kim H. B.; Sugimoto. N., Recovery of the formation and function of oxidized G-quadruplexes by a pyrene-modified guanine-tract, J. Am. Chem. Soc., 2018, 140, (17), 5774-5783, DOI:10.1021/jacs.8b01577                                                  
    Tags: 杉本A02
  15. Rode AB.; Endoh. T.; Sugimoto. N., Crowding Shifts the FMN Recognition Mechanism of Riboswitch Aptamer from Conformational Selection to Induced Fit, Angew. Chem. Int. Ed., 2018, 57, (23), 6868-6872  DOI: 10.1002/anie.201803052
    Tags: 杉本A02
  16. Meguro, T.; Terashima, N.; Ito, H.; Koike, Y.; Kii, I.; Yoshida, S.; Hosoya, T., Staudinger reaction using 2,6-dichlorophenyl azide derivatives for robust aza-ylide formation applicable to bioconjugation in living cells, Chem Commun, 2018, In press.
    DOI: 10.1039/c8cc00179k.
    Tags: 喜井 A02
  17. Saikusa, K; Osakabe, A.; Kato, D.; Fuchigami, S.; Nagadoi, A.; Nishimura, Y.; Kurumizaka, H.; Akashi, S., Structural Diversity of Nucleosomes Characterized  by Native Mass Spectrometry, Anal. Chem., 2018, 90, 8217-8226
    Doi: 10.1021/acs.analchem.8b01649
    Tags: 明石 A02
  18. Hayashi. T.; Matsuda. T.; Nagata. T.; Katahira. M.; Kinoshita. M., Mechanism of protein-RNA recognition: Analysis based on statistical mechanics of hydration, Physical Chemistry Chemical Physics, 2018, 20, 9167-9180,
    DOI: 10.1039/C8CP00155C
    Tags: 片平 A02
  19. Nishimura. H.; Kamiya. A.; Nagata. T.; Katahira. M.; Watanabe. T., Direct evidence for α ether linkage between lignin and carbohydrates in wood cell walls, Scientific Reports, 2018, 8, 6538, DOI: 10.1038/s41598-018-24328-9
    Tags: 片平 A02
  20. Kitada. A.; Kintsu. K.; Takeoka. S.; Fukami. K.; Saimura. M.; Nagata. T.; Katahira. M.; Murase. K., A Hydronium Solvate Ionic Liquid: Ligand Exchange Conduction Driven by Labile Solvation, Journal of the Electrochemical Society, 2018, 165, H496-H499
    Tags: 片平 A02
  21. Kawasaki. Y.; Kurosaki. K.; Kan. D.; Borges. K. I.; Satake. A.; Sato. M.; Kondo. K.;  Katahira. M.; Suzuki. I.; Takeda. M., Identification and characterization of the S-layer formed on the sheath of Thiothrix nivea, Archives of Microbiology, 2018, in press, DOI: 10.1007/s00203-018-1543-x
    Tags: 片平 A02
  22. Osman. W. H. W.; Lin. M.I.; Kondo. K.; Nagata. T.; Katahira. M., Characterization of the glutathione S-transferases that belong to the GSTFuA class in Ceriporiopsis subvermispora: Implications in intracellular detoxification and metabolism of wood-derived compounds, Internatiomal Journal of Biological Macromolecules, 2018, 113, 1158-1166, DOI: 10.1016/j.ijbiomac.2018.03.029
    Tags: 片平 A02
  23. Lin. M.I.; Nagata. T.; Katahira. M., High yield production of fungal manganase peroxidases by E. coli through soluble expression, Protein Expression and Purification, 2018, 145, 45-42, DOI: 10.1016/j.pep.2017.12.012
    Tags: 片平 A02
  24. Takeda. M.; Kondo. K.; Sanda. S.; Kan. D.; Borges. K. I.; Suzuki. I.; Katahira. M., Enzymatic degradation of β-1,4-linked N-acetylglucosaminoglucan prepared from Thiothrix nivea, Internatiomal Journal of Biological Macromolecules, 2018, 109, 323-328, DOI: 10.1016/j.ijbiomac.2017.12.065
    Tags: 片平 A02
  25. Watanabe. C.; Watanabe. H.; Fukuzawa. K.; Parker. L.; Okiyama. Y.; Yuki. H.;  Yokoyama. S.; Nakano. H.; Tanaka. S.; Honma. T., Theoretical Analysis of Activity Cliffs among Benzofuranone Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson-Boltzmann Surface Area (FMO+MM-PBSA) Approach, J. Chem. Inf. Model. 57 (2017) 2996-3010.
    DOI: 10.1021/acs.jcim.7b00110
    Tags: 田中 A02
  26. Okiyama. Y.; Nakano. T.; Watanabe. C.; Fukuzawa. K.; Mochizuki. Y.; Tanaka. S., Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: Implementation and DNA Study, J. Phys. Chem. B 122 (2018) 4457-4471. http://dx.doi.org/10.1021/acs.jpcb.8b01172 
    Tags: 田中 A02
  27. Xu. F.; Tanaka. S.; Watanabe. H.; Shimane. Y.; Iwasawa. M.; Ohishi. K.; Maruyama. T., Computational Analysis of the Interaction Energies between Amino Acid Residues of the Measles Virus Hemagglutinin and Its Receptors, Viruses 10 (2018) 236 (18 pages). doi: 10.3390/v10050236 Tags: 田中 A02
  28. Maruyama. K.; Sheng. Y.; Watanabe. H.; Fukuzawa. K.; Tanaka. S., Application of Singular Value Decomposition to the Inter-Fragment Interaction Energy Analysis for Ligand Screening, Comput. Theor. Chem. 1132 (2018) 23-34. https://doi.org/10.1016/j.comptc.2018.04.001
    Tags: 田中 A02

  29. Terakawa. S. M.; Lee. Y.-H.; Kinoshita. M.; Lin. Y.; Sugiki. T.; Fukui. N.; Ikenoue. T.; Kawata. Y.; Goto. Y., Membrane-induced Initial Structure of α-Synuclein Control its Amyloidogenesis on Model Membranes., Biochim. Biochem. Acta, 2018, 1860 (3), 757-766. DOI: 10.1016/j.bbamem.2017.12.011
    Tags: 後藤 A02

  30. Goto. Y.; Adachi. M.; Muta. H.; So. M., Salt-induced Formations of Partially Folded Intermediates and Amyloid Fibrils Suggests a Common Underlying Mechanism., Biophys. Rev., 2018, 10 (2), 493-502. DOI: 10.1007/s12551-017-0370-7
    Tags: 後藤 A02

  31. Micsonai. A.; Wien. E.; Bulyáki. E.; Kun. J.; Moussong. E.; Lee. Y.-H.; Goto. Y.; Réfrégiers, M.; Kardos, J., BeStSel: A Web Server for Accurate Protein Secondary Structure Prediction and Fold Recognition from the Circular Dichroism Spectra., Nucleic Acids Research, 2018, 46 (W1), W315–W322. https://doi.org/10.1093/nar/gky497
    Tags: 後藤 A02

  32. Kawauchi.  K.; Sugimoto. W.; Yasui. T.; Murata. K.; Itoh. K.; Takagi. K.; Tsuruoka. T.;  Akamatsu. K.; Tateishi-Karimata. H.; Sugimoto. N.; Miyoshi. D.,
    An anionic phthalocyanine decreases NRAS expression by breaking down its  RNA G-quadruplex Nature Communications,2018, 9, 2271                           
    Tags: 杉本A02
  33. Shankaraswamy. J.; Tyagi. S.; Singh. A.; Miyoshi. D.; Saxena. S.,
    Metal sensitive and DNA concentration dependent structural rearrangement of short oligonucleotide into large suprastructures, Journal of Biomolecular Structure & Dynamics, 2018,1-21. DOI: 10.1080/07391102.2018.1484816.  　　　
    Tags: 杉本A02
ページトップへ

Original papers A02 Group

(日本語)