分子夾雑の生命化学

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原著論文 A02班

[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.1704258114Tags: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 642–651DOI: 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 repeatdisorders under molecular crowding condition, Biochem, Biophys. Res. Commun, 2018, 496( 2 ), 601 -607 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. Trajkovsk. M.; Endoh. T.; Tateishi-Karimata. H.; Ohyama. T.; Tanaka. S.; Plavec. J.; Sugimoto. N., Pursuing origins of (poly)ethylene glycol-induced G-quadruplex structural modulations, Nucleic Acids Res., 2018, 46, 8, 4301–4315, DOI:10.1093/nar/gky250Tags: 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 DOI:10.3390/molecules22111991.Tags: 杉本A02
  13. Y. Teng, S. Pramanik, H. Tateishi-Karimata, T. Ohyama, and N. Sugimoto, 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
    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, 54, 7904-7907 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, Volume 200, Issue 8, 1257–1265, 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. colithrough soluble expression, Protein Expression and Purification, 2018, 145, 45-52, 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
  34. Hyodo, F.; Sho, T.; Basudev, M.; Fujita, K.; Tachibana, Y.; Akashi, S.; Mano, M.; Hishikawa, Y.; Matsuo, M.; Nakaji, T.; Ueno, T. Photoinduced in Vivo Magnetic Resonance Imaging (MRI) with Rapid CO Release from an MnCO-Protein Needle Composite. Chemistry. 2018, 24, 11578-11583. DOI: 10.1002/chem.201802445.  
    Tags: 明石A02
  35. Shimada, I.; Ueda, T.; Kofuku, Y.; Eddy, M.T.; Wüthrich, K.   GPCR drug discovery: integrating solution NMR data with crystal and cryo-EM structures. Nature Reviews Drug Discovery. 2018, DOI: 38/nrd.2018.180.   Tags: 上田A02
  36. Matsuura K., Synthetic Approaches to Construct Viral Capsid-like Spherical Nanomaterials, Chem. Commun., 2018, 54, 8944-8959. DOI: 10.1039/C8CC03844A
    Tags: 松浦A02
  37. Inaba H.; Matsuura K., Peptide Nanomaterials Designed from Natural Supramolecular Systems, Chem. Rec., 2018, 19,5, 843-858
    DOI: 10.1002/tcr.201800149 
    Tags: 松浦A02
  38. Zhao. C.; Song, H.; Scott. P.; Zhao, A.; Tateishi-Karimata. H.; Sugimoto. N.; Ren. J.; Qu. X., Mirror-image Dependence: Targeting Enantiomeric G-quadruplex DNA by 10 Pairs of Triplex Metallohelices, Angew. Chem. Int. Ed., 2018, 57(48), 15723-15727 DOI: 10.1002/ange.201809207 Tags: 杉本A02
  39. Teng. Y.; Tateishi-Karimata. H.; Tsuruoka. T.; Sugimoto. N., A Turn-On Detection of DNA Sequences by Means of Fluorescence of DNA-Templated Silver Nanoclusters via Unique Interactions of a Hydrated Ionic Liquid, N., Molecules, 23(11), 2889(2018) DOI:10.3390/molecules23112889 Tags: 杉本A02
  40. Teng. Y.; Tateishi-Karimata. H.; Sugimoto.N. , C-rich sequence in a non-template DNA strand regulates structure change of G-quadruplex in a template strand during transcription, , Bull. Chem. Soc. Jpn., 92(3) 572-577(2019) 
    DOI: 10.1246/bcsj.20180298
    Tags: 杉本A02
  41. Terakawa. M. S.; 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, BBA; Biomembranes, 1860(3), 757-766 (2018) 
    DOI: 10.1016/j.bbamem.2017.12.011
    Tags: 河田A02
  42. Mizobata. T.; Kawata. Y.,The versatile mutational “repertoire” of E. coliGroEL, a multi-component chaperonin nanomachine, Biophysical Review, 10 (2), 631-640 (2018) Tags: 河田A02 Lin. M.I.; Hiyama. A.; Kondo. K.; Nagata. T.; Katahira. M., Classification of fungal glucuronoyl esterases (FGEs), and characterization of two new FGEs from Ceriporiopsissubvermisporaand Pleurotus eryngii (2018) Appl. Microbiol. Biotech., 102, 9635-9645. 
    DOI: 10.1007/s00253-018-9318-5.
    Tags: 片平A02
  43. S.S.; Yamaoki. Y.; Ma. Y.; Marchand. A.; Winnerdy. F.R.; Gabelica. V.; Phan. A.T.; Katahira. M.; Nagasawa. K., Analysis of interaction between telomeric i-motif DNA and a cyclic tetraoxazole compound (2018) ChemBioChem., 19(21), 2268-2272. 
    DOI:10.1002/cbic.201800425
    Tags: 片平A02
  44. Ohara. Y.; Ozeki. Y.; Tateishi. Y.; Mashima. T.; Arisaka. F.; Tsunaka. Y.; Fujiwara. Y.; Nishiyama. A.; Yoshida. Y.; Kitadokoro. K.; Kobayashi. H.; Kaneko. Y.; Najagawa. I.; Maekura. R.; Yamamoto. S.; Katahira. M.; Matsumoto. S., Significance of a histone-like protein with its native structure for the diagnosis of asymptomatic tuberculosis (2018) PLoS ONE, 13, e0204160. 
    DOI:10.1371/journal.pone.0204160
    Tags: 片平A02
  45. Chen. Z.; Tonouchi. Y.; Matsumoto. K.; Saimura. M.; Atkin. R.; Nagata. T.; Katahira. M.;  Hagiwara. R., Partially naked fluoride in solvate ionic liquids (2018) J. Phys. Chem. Lett., 9, 6662-6667. 
    DOI: 10.1021/acs.jpclett.8b03117
    Tags: 片平A02
  46. Tokunaga. Y.; Nagata. T.; Suetomi. T.; Oshiro. S.; Kondo. K.; Katahira. M.; Watanabe. T., NMR analysis of molecular interaction of lignin with amino acid residues of carbohydrate-binding module from Trichoderma reesei Cel7A. (2019) Sci. Rep.9:1977
    DOI: 10.1038/s41598-018-38410-9
    Tags: 片平A02
  47. Wan. Osman, W. H.; Mikami. B.; Saka. N.; Kondo. K.; Nagata. T.; Katahira. M., Structure of a serine-type glutathione S-transferase of Ceriporiopsis subvermisporaand identification of the enzymatically important non-canonical residues by functional mutagenesis (2019) Biochem. Biophys. Res. Commun.510(1):177-183.
    DOI: 10.1016/j.bbrc.2019.01.076. 
    Tags: 片平A02
  48. Sheng. Y.; Watanabe. H.; Maruyama. K.; Watanabe. C.; Okiyama. Y.; Honma. T.; Fukuzawa. K.; Tanaka. S., Towards Good Correlation between Fragment Molecular Orbital Interaction Energies and Experimental IC50 for Ligand Binding: A Case Study of p38 MAP Kinase, (2018) Comput. Struct. Biotech. J.,16, 421-434. 
    DOI: 10.1016/j.csbj.2018.10.003
    Tags: 田中A02
  49. Shimamura. K.; Shimojo. F.; Nakano. A.; Tanaka. S., Ab Initio Molecular Dynamics Study of Prebiotic Production Processes of Organic Compounds at Meteorite Impacts on Ocean, (2019)J. Comput. Chem., 40(2), 349-359.
    DOI : 10.1002/jcc.25606
    Tags: 田中A02
  50. Takahashi. S.; Chelobanov. B.; Kim. K. T.; Kim. B. H.; Stetsenko. D.; Sugimoto. N.,Design and Properties of Ligand-Conjugated Guanine Oligonucleotides for Recovery of Mutated G-Quadruplexes, Molecules, 23(12), 3228,2018
    DOI: 10.3390/molecules23123228
    Tags: 杉本A02
  51. Takahashi. S.; Yamamoto. J. ; Kitamura. A.; Masataka. M. ; Sugimoto. N., Characterization of intracellular crowding environments with topology-based DNA quadruplex sensors,Anal. Chem., 91(4):2586-2590 (2019)
    DOI: 10.1021/acs.analchem.8b04177
    Tags: 杉本A02
  52.  Ghosh. S.; Takahashi. S.; Endoh. T.; Tateishi-Karimata. H.;  Hazra. S.; Sugimoto. N., Validation of the Nearest-neighbor Model for Watson–Crick Self-complementary DNA Duplexes in Molecular Crowding Condition, Nucleic Acids Res., (2019) 47, 7, 3284–3294, DOI:10.1093/nar/gkz071
    Tags: 杉本A02
  53. Takahashi. S.; Okura. H.; Sugimoto. N., Bisubstrate function of RNA polymerases triggered by molecular crowding conditions, Biochemistry,58, (8), pp 1081–1093  (2019)
    DOI: 10.1021/acs.biochem.8b01204
    Tags: 杉本A02
  54. Bhowmik. S.; Takahashi. S.; Sugimoto. N., Lighting up of thiazole orange on G-quadruplex DNA by high pressure, ACS Omega, 4(2), pp 4325–4329 (2019)
    DOI: 10.1021/acsomega.8b03430
    Tags: 杉本A02
  55. Endoh. T.; Ohyama. T.; Sugimoto. N., RNA-capturing microsphere particles (R-CAMPs) for optimization of functional aptamers, Small, 15 (2019) 1805062  
    DOI: 10.1002/smll.1805062
    Tags: 杉本A02
  56. 大山達也, 建石寿枝, 田中成典, 杉本直己, テトラエチレングリコールで修飾されたグアニン四重鎖の安定性の分子動力学計算による解析, 日本核酸化学会誌, 2018, 2, 3–10
    Tags: 杉本A02
  57. Suzuki. R.; Sakakura. M.; Mori. M.; Fujii. M.; Akashi. S.; Takahashi. H., Methyl-selective isotope labeling using α-ketoisovalerate for the yeast Pichia pastoris recombinant protein expression system. J. Biomol. NMR, 71(4), 213-223 (2018).
    DOI : 10.1007/s10858-018-0192-3.
    Tags: 明石A02
  58. Hyodo. F.; Sho. T.; Basudev. M.; Fujita. K.; Tachibana. Y.; Akashi. S.; Mano. M.; Hishikawa. Y.; Matsuo. M.; Nakaji. T.; Ueno. T., Photo-induced in Vivo MRI Imaging with Rapid CO Release from an MnCO-Protein Needle Composite. Chemistry. Eur. J., 24 (45), 11578-11583 (2018).
    DOI: 10.1002/chem.201802445
    Tags: 明石A02
  59. Tamura. R.; Oi. R.; Akashi. S.; Kaneko. M.K.; Kato. Y.; Nogi. T., Application of the NZ-1 Fab as a crystallization chaperone for PA tag-inserted target proteins. Protein Sci.28(4), 823-836 (2019). DOI : 10.1002/pro.3580
    Tags: 明石A02
  60. Hall. D.; Kinjo. A.; Goto. Y., A new look at an old view of denaturant induced protein unfolding. Anal. Biochem., 2018, 542(1), 40-57 DOI: 10.1016/j.ab.2017.11.011.
    Tags. 後藤A02
  61. Adachi. M.; Noji, M.; So. M.; Sasahara. K.; Kardos. J.; Naiki. H.; Goto. Y., Aggregation-phase diagrams of β2-microglobulin reveal temperature and salt effects on competitive formation of amyloids versus amorphous aggregates.J. Biol. Chem., 2018, 293, 14775-14785. DOI: 10.1074/jbc.RA118.004683.
    Tags. 後藤A02
  62. Noji. M.; So. M.; Yamaguchi. K.; Hojo. H.; Onda. .M.; Akazawa-Ogawa. Y.; Hagihara. Y.; Goto. Y., Heat-induced aggregation of hen ovalbumin suggests a key factor responsible for serpin polymerization. Biochemistry, 2018, 57(37), 5415-5426. 
    DOI: 10.1021/acs.biochem.8b00619.
    Tags. 後藤A02
  63. Kakuda. K.; Ikenaka. K.; Araki. K.; So. M.; Aguirre. C.; Kajiyama. Y.; Konaka. K.; Noi. K.; Baba. K.; Tsuda. H.; Nagano. S.; Ohmichi. T.; Nagai. Y.; Tokuda. T.; El-Agnaf. O.; Ogi. H.; Goto. Y.; Mochizuki. H., Ultrasonication-based rapid amplification of α-synuclein aggregates in cerebrospinal fluid. Scientific Reports, 2019, 9, 6001 DOI: 10.1038/s41598-019-42399-0.
    Tags. 後藤A02
  64. Nakasone, Y.; Kikukawa, K.; Masuda, S.; Terazima, M. Time-Resolved Study of Interprotein Signaling Process of a Blue Light Sensor PapB-PapA Complex, J Phys Chem B, 2019, 123(15), 3210-3218. DOI: 10.1021/acs.jpcb.9b00196. Tags: 中曽根A02
  65. Zhang, C., Yamaguchi1, Y., So, M., Sasahara, K., Ito, T., Yamamoto, S., Narita, I., Kardos, J., Naiki, H., and *Goto, Y. Possible mechanisms of polyphosphate-induced amyloid fibril formation of β2-microglobulin. Proc. Natl. Acad. Sci. USA
    2019 116 (26) 12833-12838
    DOI: 10.1073/pnas.1819813116
    Tags: 後藤A02
  66. Iida. M.; Mashima. T.; Yamaoki. Y.; So. M.; Nagata. T.; Katahira, M., The anti-prion RNA aptamer R12 disrupts the Alzheimer’s disease-related complex between prion and amyloid β, FEBS J., 286, 2355-2365, DOI:10.1111/febs.14819.
    Tags: 片平A02
  67. Wan Osman. W. H.;  Mikami. B.; Saka. N.; Kondo. K.; Lin. M. I.; Nagata. T.; Katahira, M., Identification of key residues for activities of atypical glutathione S-transferase of Ceriporiopsis subvermispora, a selective degrader of lignin in woody biomass, by crystallography and functional mutagenesis, Int. J. Biol. Macromol., 132, 222-229, 
    DOI: 10.1016/j.ijbiomac.2019.03.199.
    Tags: 片平A02
  68. Wan, L., Kamba, K., Nagata, T. and Katahira, M., An insight into the dependence of the deaminase activity of human APOBEC3F on the length of single-stranded DNA, which is affected by the concentrations of APOBEC3F and single-stranded DNA, Biochim. Biophys. Acta,2020 Feb;1864(2):129346
    DOI: 10.1016/j.bbagen.2019.04.011.
    Tags: 片平A02
  69. Matsuura. K.; Honjo. T., Artificial Viral Capsid dressed up with Human Serum Albumin, Bioconjugate Chem., 30(6), 1636-1641, 2019. 
    DOI: 10.1021/acs.bioconjchem.9b00327.
    Tags: 松浦A02
  70. Kohyama. S.; Yoshinaga. N.; Yanagisawa. M.; Fujiwara. K.; Doi. N., Cell-sized confinement controls generation and stability of a protein wave for spatiotemporal regulation in cells. eLife, 2019;8:e44591, DOI: 10.7554/eLife.44591
    Tags: 藤原A02
  71. Nakasone. Y.; Takaramoto. S.; Terazima. M., Time-Resolved Diffusion Detection with Microstopped Flow System. Anal Chem.2019;91(18):11987-11993. doi: 10.1021/acs.analchem.9b02897.
    Tags: 中曽根A02
  72. Nakano. S; Ayusawa. T.; Tanino. Y.; Sugimoto. N., Stabilization of DNA Loop Structures by Large Cations, J Phys Chem B., 123(36), 7687-7694 (2019)
    DOI: 10.1021/acs.jpcb.9b06074
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  73. Kuwahara. M.; Fujita. H.; Kataoka. Y;  Nakajima. Y.; Yamada. M.; Sugimoto. N.,
    In situ condensation of an anti-cancer drug into fibrin gel enabling effective inhibition of tumor cell growth Chem Commun(Camb), 55, 11679-11682 (2019)
    DOI: 10.1039/C9CC06418D
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  74. Takahashi. S.; Bhattachargee. S.; Ghosh. S.; Sugimoto. N.; Bhowmik. S., Preferential targeting cancer-related i-motif DNAs by the plant flavonol fisetin for theranostics applications, Sci Rep., 10, 2504 (2020)
    DOI : 10.1038/s41598-020-59343-2
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  75. Yoshida. A.; Kohyama. S.; Fujiwara. K.; Nishikawa. S.; Doi. N.,
    Regulation of spatiotemporal patterning in artificial cells by a defined protein expression system
    Chemical Science, 2019, 10, 11064-11072
    DOI: 10.1039/C9SC02441G
    Tags: 藤原A02
  76. Tokuda, E.; Takei, Y.; Ohara, S.; Fujiwara, N.; Hozumi, I.; Furukawa, Y. Wild-type Cu/Zn-superoxide dismutase is misfolded in cerebrospinal fluid of sporadic amyotrophic lateral sclerosis. Molecular Neurodegeneration, 2019, 14, 42 
    DOI: 10.1186/s13024-019-0341-5
    Tags: 古川A02
  77. Takaramoto. S.; Nakasone. Y.; Sadakane. K.; Maruta. S.; Terazima. M., 
    Spiropyran labeling for sensitive probing of protein diffusion by the transient grating method.
    Chemical Physics Letters.Volume 739, January 2020, 136919
    DOI: 10.1016/j.cplett.2019.136919 Tags: 中曽根A02
  78. Yusuke. N.; Ohshima M.; Okajima. K.; Tokutomi. S.; Terazima. M.,
    Photoreaction Dynamics of Full-Length Phototropin from Chlamydomonas Reinhardtii
    J. Phys. Chem. B.  2019, 123, 51, 10939-10950
    DOI: 10.1021/acs.jpcb.9b09685 Tags: 中曽根A02
  79. Aoki. D.; Nomura. K.; Hashiura. M.; Imamura. Y.; Miyata. S.; Terashima. N.; Mstsushita. Y.; Nishimura. H.; Watanabe. T.; Katahira. M.; Fukushima. K.,
    Evaluation of ring-5 structures of guaiacyl lignin in Ginko bilobaL. using solid- and liquid-state 13C NMR difference spectroscopy
    Holzforschung, 73, 1083-1092 DOI:org/10.1515/hf-2019-0011
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  80. Yamada. T.; Hayashi. T.; Hikiri. S.; Kobayashi. N.; Yanagawa. H.; Ikeuchi. M.; Katahira. M.; Nagata. T.; Kinoshita. M., How does the recently discovered peptide MIP exhibit much higher binding affinity than an anticancer protein p53 for an oncoprotein MDM2?
    J. Chem. Inform. & Model., 59, 3533-3544. DOI: 10.1021/acs.jcim.9b00226
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  81. Higashi. S. L.; Shibata. A.; Kitamura. Y.; Hirosawa. K. M.; Suzuki. K. G. N.; Matsuura. K.; Ikeda. M., Hybrid Soft Nanomaterials Composed of DNA Microspheres and Supramolecular Nanostructures of Semi-artificial Glycopeptides, Chem. Eur. J., 25 (51), 11955-11962, 2019.
    DOI: 10.1002/chem.201902421.
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  82. Matsuura, K.; Ota, J.; Fujita, S.; Shiomi, Y.; Inaba, H., AConstruction of Ribonuclease-Decorated Artificial Virus-like Capsid by Peptide Self-assembly, J. Org. Chem.,2020, 85, 3, 1668-1673
    DOI: 10.1021/acs.joc.9b02295.
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  83. Teng. Y.; Tateishi-Karimata. H.; Ohyama. T.; Sugimoto. N., Effect of Potassium Concentration on Triplex Stability under Molecular Crowding Conditions
    Molecules, 25, 387 (2020)
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  84. Tateishi-Karimata. H.; Ohyama. T.; Muraoka. T.; Tanaka. S.; Kinbara. K.; Sugimoto. N., New Modified Deoxythymine with Dibranched Tetraethylene Glycol Stabilizes G-Quadruplex Structures
    Molecules, 25, 705 (2020)
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  85. H. Tateishi-Karimata and N. Sugimoto
    Chemical biology of non-canonical structures of nucleic acids for therapeutic applications, Chem. Commun., 2020, 56, 2379-2390
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  86. Tateishi-Karimata. H.; Banerjee. D.; Ohyama. T.; Matsumoto. S.; Miyoshi. D.;  Nakano. S.; Sugimoto. N., Hydroxyl groups in cosolutes regulate the G-quadruplex topology of telomeric DNA, Biochem. Biophys. Res. Commun., 523, 1(23), 177-183
    DOI: 10.1016/j.bbrc.2020.02.045
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  87. Kovačič1. M.; Podbevšek. P.; Tateishi-Karimata. H.; Takahashi. S.; Sugimoto. N.; Plavec.J., Thrombin binding aptamer G-quadruplex stabilized by pyrene-modified nucleotides, Nucleic Acids Res, 48,7,3975–3986
     DOI: 10.1093/nar/gkaa118
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  88. Araki, K.; Yagi, N.; Aoyama, K.; Choong, C.; Hayakawa H.; Fujimura, H.; Nagai, Y.; Goto, Y.; Mochizuki, H., Parkinson’s disease is a type of amyloidosis featuring accumulation of amyloid fibrils of α-synuclein, Proc. Natl. Acad. Sci. USA, 116, 17963-17969 (2019).
    DOI: 10.1073/pnas.1906124116
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  89. Sasahara, K.; Yamaguchi, K.; So, M.; Goto, Y., Polyphosphates diminish solubility of a globular protein and thereby promote amyloid aggregation, J. Biol. Chem., 294, 15318-15329 (2019).
    DOI: 10.1074/jbc.RA119.008662
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  90. Noji, M.; Sasahara, K.; Yamaguchi, K.; So, M.; Sakurai, K.; Kardos, J.; Naiki, H.; Goto, Y., Heating during agitation of β2-microglobulin reveals that supersaturation breakdown is required for amyloid fibril formation at neutral pH, J. Biol. Chem., 294, 15826-15835 (2019).
    DOI:10.1074/jbc.RA119.009971
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  91. Muta, H.; So, M.; Sakurai, K.; Kardos, J.; Naiki, H.; Goto, Y., Amyloid formation under complicated conditions in which β2-microglobulin coexists with its proteolytic fragments, Biochemistry, 58, 4925-4934 (2019).
    DOI: 10.1021/acs.biochem.9b00917
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  92. Taricska, N.; Horváth, D.; Menyhárd, D. K.; Ákontz-Kiss, H.; Noji, M.; So, M.; Goto, Y.; Fujiwara, T.; Perczel, A., The route from the folded to the amyloid state: exploring the potential energy surface of a drug-like miniprotein, Chem. European J., 26, 1968-1978 (2020).
    DOI: 10.1002/chem.201903826
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  93. Furukawa, K.*; Aguirre, C.*; So, M.*; Sasahara, K.; Miyanoiri, Y.; Sakurai, K.; Yamaguchi, K.; Ikenaka, K.; Mochizuki, H.; Kardos, J.; Kawata, Y.; Goto, Y. (*equal contribution), Isoelectric point-amyloid formation of α-synuclein extends the solubility and supersaturation-limited mechanism, Curr. Res. Struct. Biol., 10, 35-44 (2020).
    DOI: 10.1016/j.crstbi.2020.03.001
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  94. Sawada. M.; Yamaguchi. K.; Hirano. M.; Noji. M.; So. M.; Otzen. D.; Kawata. Y.; Goto. Y., Amyloid formation of alpha-synuclein based on the solubility- and supersaturation-dependent mechanism, Langmuir, (2020), 36(17):4671-4681.
    DOI: 10.1021/acs.langmuir.0c00426.
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  95. Tokunaga. Y.; Takeuchi. K.; Okude. J.; Ori. K; Torizawa. T; Shimada. I;, Structural Fingerprints of an Intact Monoclonal Antibody Acquired under Formulated Storage Conditions via 15N Direct Detection Nuclear Magnetic Resonance, J Med Chem. 63, 5360-5366. (2020)
    Doi: 10.1021/acs.jmedchem.0c00231.
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  96. Endoh. T.; Sugimoto. N., Conformational Dynamics of the RNA G-Quadruplex and its Effect on Translation Efficiency Molecules, 24, 1613 (2019).
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  97. Takahashi. S.; Sugimoto. N., Quantitative Analysis of Stall of Replicating DNA Polymerase by G-Quadruplex Formation Methods Mol. Biol. (Springer), 2035, 257-274 (2019). 
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  98. S. Ghosh, S. Takahashi, T. Ohyama, T. Endoh, H. Tateishi-Karimata, and N. Sugimoto
    Universal Nearest-Neighbor Parameters for DNA Duplex Stability under Molecular Crowding Conditions
    Proc. Natl. Acad. Sci. USA.(2020),117(25):14194-14201
    DOI:10.1073/pnas.1920886117.                                                                            
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  99. S. Matsumoto, H. Tateishi-Karimata, S. Takahashi, T. Ohyama, and N. Sugimoto
    Effect of molecular crowding on the stability of RNA G-quadruplexes with various numbers of quartets and lengths of loops
    Biochemistry, 59(28), 2640–2649 (2020)
    DOI:10.1021/acs.biochem.0c00346                                                                                           Tags:杉本 A02
  100. Dornheim, T.; Sjostrom, T.; Tanaka, S.; Vorberger, J., Strongly Coupled Electron Liquid: Ab Initio Path Integral Monte Carlo Simulations and Dielectric Theories, Phys. Rev. B 101 (2020) 045129. Tags: 田中A02
  101. Umegaki, T.; Tanaka, S., Nanoscale Quantum Thermal Conductance at Water Interface: Green’s Function Approach Based on One-Dimensional Phonon Model,
    Molecules 25 (2020) 1185. Tags: 田中A02
  102. Suzuki, Y.; Watanabe, H.; Okiyama, Y.; Ebina, K.; Tanaka, S., Comparative Study on Model Parameter Evaluations for the Energy Transfer Dynamics in Fenna-Matthews-Olson Complex, Chem. Phys. 539 (2020) 110903. Tags: 田中A02
  103. Tanaka, S.; Watanabe, C.; Honma, T.; Fukuzawa, K.; Ohishi, K.; Maruyama, T., Identification of Correlated Inter-Residue Interactions in Protein Complex Based on the Fragment Molecular Orbital Method, J. Mol. Graph. Model. 100 (2020) 107650. Tags: 田中A02
  104. Tanaka, S.; Shimamura, K., Temperature Relaxation in Binary Hard-Sphere Mixture System: Molecular Dynamics and Kinetic Theory Study, J. Chem. Phys. 153 (2020) 034114. Tags: 田中A02
  105. Mizukoshi. Y.; Takeuchi. K.; Tokunaga. Y.; Matsuo. H.; Imai. M.; Fujisaki. M.; Kamoshida. H.; Takizawa. T.; Hanzawa. H.; Shimada. I., Targeting the cryptic sites: NMR-based strategy to improve protein druggability by controlling the conformational equilibrium. Sci Adv., 2020, 6:eabd0480. doi: 10.1126/sciadv.abd0480. 
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  106. Takahashi. H.; Yanamisawa. A.; Kajimoto. S.; Nakabayashi. T., Observation of the changes in the chemical composition of lipid droplets using Raman microscopy. Phys. Chem. Chem. Phys., 2020, 22, 21646-21650.
    Doi: 10.1039/d0cp03805a. 
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  107. Kohyama, S.;Fujiwara, K; Yoshinaga, N; Doi, N., Conformational equilibrium of MinE regulates allowable concentration ranges of a protein wave for cell division, Nanoscale., 2020, 12:11960 – 11970. doi: 10.1039/D0NR00242A
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  108. Kohyama, S.;Fujiwara, K; Yoshinaga, N; Doi, N., Self-Organization Assay for Min Proteins of Escherichia coli in Micro-droplets Covered with Lipids, bio-protocol, 2020, 10(6): e3561, doi: 10.21769/BioProtoc.3561
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  109. Yuzu. K.; Yamamoto. N.; Noji. M.; So. M.; Goto. Y.; Iwasaki. T.; Tsubaki. M.; Chatani. E., Multistep changes in amyloid structure induced by cross-seeding on a rugged energy landscape, Biophys. J., 2020, DOI: 10.1016/j.bpj.2020.12.005
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  110. Mizuno. H.; Hoshino. J.; So. M.; Kogure. Y.; Fujii. T.; Ubara. Y.; Takaichi. K.; Nakaniwa. T.; Tanaka. H.; Kurisu. G.; Kametani. F.; Nakagawa. M.; Yoshinaga. T.; Sekijima. Y.; Higuchi. K.; Goto. Y.; Yazaki. M., Dialysis-related amyloidosis associated with a novel β2-microglobulin variant, Amyloid, 2020, DOI: 10.1080/13506129.2020.1813097
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  111. Nakajima. K.; Yamazaki. T.; Kimura. Y.; So. M.; Goto. Y.; Ogi. H., Time-resolved observation of evolution of amyloid-β oligomer with temporary salt crystals, J. Pyhs. Chem. Lett., 2020, 11(15), 6176-6184. DOI: 10.1021/acs.jpclett.0c01487
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  112. Okuwaki. R.; Shinmura. I.; Morita. S.; Matsugami. A.; Hayashi. F.; Goto. Y.; Nishimura. C., Distinct residual and disordered structures of alpha-synuclein analyzed by amide-proton exchange and NMR signal intensity, Biochim Biophys Acta – Proteins and Proteomics, 2020, 1868(9), 140464. DOI: 10.1016/j.bbapap.2020.140464
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  113. Ito. T.; Yamamoto. S.; Yamaguchi. K.; Sato. M.; Kaneko. Y.; Goto. S.; Goto. Y.; Narita. I., Inorganic polyphosphate potentiates lipopolysaccharide-induced macrophage inflammatory response, J. Biol. Chem., 2020, 295(12), 4014-4023. DOI: 10.1074/jbc.RA119.011763
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  114. Kanemura, S.; Sofia, F. E.; Hirai, N.; Okumura, M.; Kadokura, H.; Inaba, K., Characterization of the ER-resident peroxidases GPx7 and GPx8 shows the higher oxidative activity of GPx7 and its linkage to oxidative protein folding. J. Biol. Chem. 2020, 295, 12772-12785.
    DOI: 10.1074/jbc.RA120.013607.
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  115. Ninagawa, S.; Tada, S.; Okumura, M.; Inoguchi, K.; Kinoshita, M.; Kanemura, S.; Imami, K.; Umezawa, H.; Ishikawa, T.; Mackin, R.; Torii, S.; Ishihama, Y.; Inaba, K.; Anazawa, T.; Nagamine, T.; Mori, K., Antipsychotic olanzapine-induced misfolding of proinsulin in the endoplasmic reticulum accounts for atypical development of diabetes. eLife 2020 9, e60970.
    DOI: 10.7554/eLife.60970.
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  116. Okumura, M.; Noi, K.; Inaba, K., Visualization of structural dynamics of protein disulfide isomerase enzymes in catalysis of oxidative folding and reductive unfolding. Curr. Opin. Struct. Biol. 2020 66, 49-57.
    DOI: 10.1016/j.sbi.2020.10.004.
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  117. Kanemura, S.; Matsusaki, M.; Inaba, K; Okumura, M., PDI family members as guides for client folding and assembly. Int. J. Mol. Sci. 2020 21, E9351.
    DOI: 10.3390/ijms21249351.
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  118. Matsusaki, M.; Kanemura, S.; Kinoshita, M.; Lee, Y.H.; Inaba, K.; Okumura, M., The protein disulfide isomerase family: from proteostasis to pathgenesis. BBA. General Subject 2020 1864(2) 129338.
    DOI: 10.1016/j.bbagen.2019.04.003.
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  119. Saio, T.; M. Okumura.; Y.H. Lee., Solution NMR for investigation of liquid-liquid phase separation. Journal of the Korean Magnetic Resonance Society 2020 24 47-52.
    DOI: 10.6564/JKMRS.2020.24.2.047.
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  120. Arai, A.; Watanabe, R.; Hattori, A.; Iio, K.; Hu, Y.; Yoneda, K.; Kigoshi, H.; Kita, M., N,N-Dimethylaminopyrene as a fluorescent affinity mass tag for ligand-binding mode analysis. Sci. Rep. 2020, 10, 7311. DOI: 10.1038/s41598-020-64321-9. Tags: 北 A02
  121. Hirukawa, M.; Zhang, M.; Echenique–Diaz, L. M.; Mizota, K.; Ohdachi, S. D.; Begué–Quiala, G.; Delgado–Labañino, J. L.; Gámez–Díez, J.; Alvarez–Lemus, J.; Galano Machado, L.; Suárez Núñez, M.; Shibata, T.; Kigoshi, H.; Kita, M. Isolation and structure-activity relationship studies of jacaranones: anti-inflammatory quinoids from the Cuban endemic plant Jacaranda arborea (Bignoniaceae). Tetrahedron Lett. 2020, 61, 152005. DOI: 10.1016/j.tetlet.2020.152005. Tags: 北 A02
  122. Zhang, M.; Sunaba, T.; Sun, Y.; Shibata, T.; Sasaki, K.; Isoda, H.; Kigoshi, H.; Kita, M. Acyl-CoA dehydrogenase long chain (ACADL) is a target protein of stylissatin A, an anti-inflammatory cyclic heptapeptide. J. Antibiot. 2020, 73, 589-592. DOI: 10.1038/s41429-020-0322-5. Tags: 北 A02
  123. Noji, M.; Samejima, T.; Yamaguchi, K.; So, M.; Yuzu, K.; Chatani, E.; Akazawa-Ogawa, Y.; Hagihara, Y.; Kawata, Y.; Ikenaka, K.; Mochizuki, H.; Kardos, J.; Otzen, D. E.; Bellotti, V.; Buchner, J.; Goto, Y., Breakdown of supersaturation barrier links protein folding to amyloid formation, Commun. Biol. 2021, 4(120), 1-10. DOI: 10.1038/s42003-020-01641-6  Tags: 後藤A02

  124. Furukawa, H.; Inaba, H.; Inoue, F.; Sasaki, Y.; Akiyoshi, K.; Matsuura, K., Enveloped Artificial Viral Capsids Self-assembled from Anionic β-Annulus Peptide and Cationic Lipid Bilayer, Chem. Commun. 56, 7092–7095 (2020). DOI: 10.1039/D0CC02622K. Tags: 松浦A02

  125. Matsuura, K.; Shiomi, Y.; Mizuta, T.; Inaba, H., Horseradish Peroxidase-Decorated Artificial Viral Capsid Constructed from b-Annulus Peptide via Interaction between His-Tag and Ni-NTA, Processes, 8(11), 1455 (2020). DOI: 10.3390/pr8111455. Tags: 松浦A02
  126. Nakamura, Y.; Sato, Y.; Inaba, H.; Iwasaki, T.; Matsuura, K., Encapsulation of mRNA into artificial viral capsids via hybridization of a b-annulus-dT20 conjugate and the poly(A) tail of mRNA, Appl. Sci. 10(22), 8004 (2020). DOI: 10.3390/app10228004. Tags: 松浦A02
  127. Higashi, S. L.; Hirosawa, K. M.;  Suzuki, K. G.N.;  Matsuura, K.;  Ikeda, M.,  One-Pot Construction and Fluorescence Imaging of Multicomponent Supramolecular Materials Comprising Self-Sorted Supramolecular Architectures of DNA and Semi-Artificial Glycopeptides, ACS Applied Bio Materials, 3(12), 9082-9092 (2020). DOI: 10.1021/acsabm.0c01316. Tags: 松浦A02
  128. S.Takahashi, H. Okura, P. Chilika, S. Ghosh, and N. Sugimoto

    Molecular crowding induces primer extension by RNA polymerase through base stacking beyond Watson–Crick rules,RSC Adv., 10, 33052-33058 (2020) [Selected as a HOT Article]
    Tags:杉本 A02

  129. S.Takahashi, P. Herdwijn, and N. Sugimoto
    Effect of Molecular Crowding on DNA Polymerase Reactions along Unnatural DNA Templates,Molecules, 25, 4120 (2020)
    Tags:杉本 A02

  130. D.Banerjee, H. Tateishi-Karimata, T. Ohyama, S. Ghosh, T. Endoh, S. Takahashi, and N. Sugimoto
    Improved nearest-neighbor parameters for the stability of RNA/DNA hybrids under a physiological condition,Nucleic Acids Res., 48, 12042-12054 (2020) [Selected as a Cover]
    Tags:杉本 A02

  131. S.Lathwal, S. S. Yerneni, S. Boye, U. L. Muza, S. Takahashi, N. Sugimoto, A. Lederer, S. R. Das, P. G. Campbell, and K. Matyjaszewski,Engineering exosome polymer hybrids by atom transfer radical polymerization,Proc. Natl. Acad. Sci. U. S. A., 118, e2020241118 (2021)
    Tags:杉本 A02

  132. 杉本渉、川内敬子、三好大輔
    RAS mRNAを狙った分子標的型光線力学療法
    Medical Science Digest, 46 (9), 26-27（2020）
    Tags:杉本 A02

  133. Kazuki Kohata, Daisuke Miyoshi   
    RNA Phase Separation-Mediated Direction of Molecular Trafficking Under Conditions of Molecular Crowding doi: 10.1007/s12551-020-00696-3 
    Biophys. Rev., 12(3), 669–676（2020）
    Tags:杉本 A02

  134. Takeru Torii, Wataru Sugimoto, Keiko Kawauchi, Daisuke Miyoshi    
    Novel Strategy of Photodynamic Therapy Targeting RAS mRNA with G-Quadruplex Ligands for Cancer Treatment          
    J Data Mining Genomics Proteomics, 11(2), No:1000226 （2020）
    Tags:杉本 A02

  135. Keiko Kawauchi, Ryoto Urano, Natsuki Kinoshita, Shin Kuwamoto, Takeru Torii, Yoshiki Hashimoto, Shinya Taniguchi, Mitsuki Tsuruta, Daisuke Miyoshi            
    Photosensitizers Based on G-Quadruplex Ligand for Cancer Photodynamic Therapy   
    Genes, 11 (11), 1340; doi.org/10.3390/genes11111340（2020）
    Tags:杉本 A02

  136. Mitsuki Tsuruta, Yui Sugitani, Naoki Sugimoto, D andDaisuke Miyoshi            
    Combined Effects of Methylated Cytosine and Molecular Crowding on the Thermodynamic Stability of DNA Duplexes            
    Int. J. Mol. Sci. , 22(2), 947 https://doi.org/10.3390/ijms22020947（2021）
    Tags:杉本 A02

  137. Choi. S.; Nakasone. Y.; Hellingwerf. K.; Terazima. M., Photoreaction Dynamics of a Full-Length Protein YtvA and Intermolecular Interaction with RsbRA, Biochemistry, 59(50), 4703-4710.
    DOI: 10.1021/acs.biochem.0c00888. (2020) 
    Tags:中曽根 A02
  138. Kim. S.; Nakasone. Y.; Takakado. A.; Yamazaki. Y.; Kamikubo. H.; Terazima. M., Wavelength-Dependent Photoreaction of PYP from Rhodobacter capsulatus, Biochemistry, 59(51), 4810-4821.
    DOI: 10.1021/acs.biochem.0c00821. (2020) 
    Tags:中曽根 A02
  139. Takaramoto. S.; Nakasone. Y.; Sadakane. K.; Maruta. S.; Terazima. M., 
    Time-resolved detection of SDS-induced conformational changes in α-synuclein by a micro-stopped-flow system      
    RSC Advances, 11(2), 1086-1097.
    DOI: 10.1039/D0RA09614H. (2021)
    Tags:中曽根 A02
  140. Satopathi. S.; Endoh. T.;  Podbevšek. P.; Plavec. J.; Sugimoto. N.,

    Transcriptome screening followed by integrated physicochemical and structural analyses for investigating RNA-mediated berberine activity
    Nucleic Acids Res., 2021, gkab189 (2021)
    Tags:杉本 A02

  141. Okada. S.; Matsusaki. M.; Okumura. M.; and Muraoka. T., Conjugate of Thiol and Guanidyl Units with Oligoethylene Glycol Linkage for Manipulation of Oxidative Protein Folding. 
    molecules 26 879 (2021)
    Tags: 奥村A02
  142. Hirayama. C.; Machida. K.; Noi. K.; Murakawa. T.; Okumura. M.; Ogura. T.; Imataka. H.; Inaba. K., Distinct roles and actions of protein disulfide isomerase family enzymes in catalysis of co-translational disulfide bond formation.
    iScience 4 102296 (2021)
    Tags: 奥村A02
  143. Okumura. M.; Kanemura. S.; Matsusaki. M.; Kinoshita. M.; Saio. T.; Ito. D.; Hirayama. C.; Kumeta. H.; Watabe. M.; Amagai. Y.; Lee. Y.H.; Akiyama. S.; Inaba. K., A unique leucine-valine adhesive motif supports structure and function of protein disulfide isomerase P5 via dimerization.
    Structure 29 1-14 (2021)
    Tags: 奥村A02
  144. Tanikawa. Y.; Kanemura. S.; Ito. D.; Lin. Y.; Matsusaki. M.; Kuroki. K.; Yamaguchi. H.; Maenaka. K.; Lee. Y.H.; Inaba. K.; Okumura. M., Ca2+ regulates ERp57-calnexin complex formation. molecules 26 2853 (2021)
    Tags: 奥村A02
  145. Murakami, K.; Kajimoto, S.; Shibata, D.; Kuroi, K.; Fujii, F.; Nakabayashi, T., Observation of liquid-liquid phase separation of ataxin-3 and quantitative evaluation of its concentration in a single droplet using Raman microscopy, Chemical Sciences, 2021, 12, 7411-7418. DOI: 10.1039/D0SC06095J Tags: 梶本 A02
  146. Shibata, D.; Kajimoto, S.; Nakabayashi, T., Label-free tracking of intracellular molecular crowding with cell-cycle progression using Raman microscopy, Chemical Physics Letters, 2021, 779, 138843 DOI: 10.1016/j.cplett.2021.138843. 
    Tags: 梶本 A02
  147. Kuramochi. M.; Omata. H.; Ishihara. M.; Hanslin. ØS.; Mizumaki. M.; Kawamura. N.; Osawa. H.; Suzuki. M.; Mio. K.; Sekiguchi. H.; Sasaki. C. Y., Tilting and rotational motions of silver halide crystal with diffracted X-ray blinking, Scientific Reports, 2021, 11, 4097. DOI: 10.1038/s41598-021-83320-y
    Tags: 倉持 A02
  148. Chang. J.; Baek. Y.; Lee. I.; Sekiguchi. H.; Ichiyanagi. K.; Mio. K.; Nozawa. S.; Fukaya. R.; Adachi. S.; Kuramochi. M.; Sasaki. C. Y., Diffracted X-ray blinking measurements of interleukin 15 receptors in the inner/outer membrane of living NK cells, Biochemical and Biophysical Research Communications, 2021, 556, 53–58. DOI: 10.1016/j.bbrc.2021.03.144
    Tags: 倉持 A02
  149. Arai. T.; Inamasu. R.; Yamaguchi. H.; Sasaki. D.; Sato-Tomita. A.; Sekiguchi. H.; Mio. K.; Tsuda. S.; Kuramochi. M.; Sasaki. C. Y., Laboratory Diffracted X-ray Blinking to Monitor Picometer Motions of Protein Molecules and Application to Crystalline Materials., Structural Dynamics, 2021, 8, 044302. DOI: 10.1063/4.0000112
    Tags: 倉持 A02
  150. Shinkai. Y.; Kuramochi. M.; Miyafusa. T., New Family Members of FG Repeat Proteins and Their Unexplored Roles During Phase Separation., Front. Cell Dev. Biol., 2021, 9, 708702. DOI: 10.3389/fcell.2021.708702
    Tags: 倉持 A02
  151. Matsuura. K.; Fujita. S., A Photoresponsive Artificial Viral Capsid Self-Assembled from an Azobenzene-Containing β-Annulus Peptide, Int. J. Mol. Sci., 22, 4028 (2021). DOI:10.3390/ijms22084028. 
    Tags: 松浦 A02

  152. Kobayashi. R.; Inaba. H.; Matsuura. K., Fluorescence Correlation Spectroscopy Analysis of Effect of Molecular Crowding on Self-Assembly of β-Annulus Peptide into Artificial Viral Capsid, Int. J. Mol. Sci., 22, 4754 (2021)
    DOI: 10.3390/ijms22094754. 
    Tags: 松浦 A02

  153. Tateishi-Karimata. H.; Sugimoto. N., Roles of non-canonical structures of nucleic acids in cancer and neurodegenerative diseases, Nucleic Acids Res.,49, in press (2021)
    Tags:杉本A02

  154. Endoh. T.; Brodyagin. N.; Hnedzko. D.; Sugimoto. N.; Rozners. E., Triple-Helical Binding of Peptide Nucleic Acid Inhibits Maturation of Endogenous MicroRNA-197

    ACS Chem. Biol., 16, 1147-1151 (2021) [Selected as a Front Cover]
    Tags:杉本 A02

  155. Shibata. K.; Nakasone. Y.; Terazima. M., 
    Enzymatic activity of the blue light-regulated phosphodiesterase BlrP1 from Klebsiella pneumoniae shows a nonlinear dependence on light intensity      
    FEBS Lett. 2021, 595(10):1473-1479. doi: 10.1002/1873-3468.14073. 
    Tags:中曽根 A02
  156. Ikoma. M.; Nakasone. Y.; Terazima. M.,
    Photoreaction of photoactivated adenylate cyclase from cyanobacterium Microcoleus chthonoplastes    
    J Photochem Photobiol B. 2021, 221:112252. doi: 10.1016/j.jphotobiol.2021.112252.
    Tags:中曽根 A02
  157. Nakasone. Y.; Terazima. M.,
    A Time-Resolved Diffusion Technique for Detection of the Conformational Changes and Molecular Assembly/Disassembly Processes of Biomolecules 
    Front Genet. 2021, 12:691010. doi: 10.3389/fgene.2021.691010. 
    Tags:中曽根 A02
  158. Yamamoto. S.; Sasahara. K.; Domon. M.; Yamaguchi. K.; Ito. T.; Goto. S.; Goto. Y.; Narita. I., pH-Dependent protein binding properties of uremic toxins in vitro, Toxins (Basel), 2021, 13(2), 116. DOI: 10.3390/toxins13020116.
    Tags:後藤 A02
  159. Nakajima. K.; Noi. K.; Yamaguchi. K.; So. M.; Ikenaka. K.; Mochizuki. H.; Ogi. H.; Goto. Y., Optimized sonoreactor for accelerative amyloid-fibril assays through enhancement of primary nucleation and fragmentation, Ultrason. Sonochem., 2021, 73, 105508. DOI:10.1016/j.ultsonch.2021.105508.
    Tags:後藤 A02
  160. Yamaguchi. K.; So. M.; Aguirre. C.; Ikenaka. K.; Mochizuki. H.; Kawata. Y.; Goto. Y., Polyphosphates induce amyloid fibril formation of α-synuclein in concentration-dependent distinct manners, J. Biol. Chem., 2021, 296, 100510. DOI:10.1016/j.jbc.2021.100510.
    Tags:後藤 A02
  161. Chatani. E.; Yuzu. K.; Ohhashi. Y.; Goto. Y., Current understanding of the structure, stability and dynamic properties of amyloid fibrils, Int. J. Mol. Sci., 2021, 22(9), 4349. DOI:10.3390/ijms22094349.
    Tags:後藤 A02
  162. So. M.; Kimura. Y.; Yamaguchi. K.; Sugiki. T.; Fujiwara. T.; Aguirre. C.; Ikenaka. K.; Mochizuki. H.; Kawata. Y.; Goto. Y., Polyphenol-solubility alters amyloid fibril formation of α-synuclein, Protein Sci., 2021, 30(8), 1701-1713. DOI:10.1002/pro.4130.
    Tags:後藤 A02
  163. Noi. K,; Ikenaka. K.; Mochizuki. H.; Goto. Y.; Ogi. H., Disaggregation behavior of amyloid β fibrils by anthocyanins studied by total-internal-reflection-fluorescence microscopy coupled with a wireless quartz-crystal microbalance biosensor, Anal. Chem., 2021, DOI: 10.1021/acs.analchem.1c01720.
    Tags:後藤 A02
  164. Yang, Q.; Kajimoto, S.; Kobayashi, Y.; Hiramatsu H.; Nakabayashi, T., Regulation of cell volume by nanosecond pulsed electric fields, J. Phys. Chem. B, 2021, 125, 10692-10700, DOI: 10.1021/acs.jpcb.1c06058
    Tags: 梶本 A02
  165. Akui, T.; Fujiwara, K.; Sato, G.; Takinoue, M.; Nomura, S.M.; Doi N., System concentration shift as a regulator of transcription-translation system within liposomes, iScience, 2021, 24(8), 102859, DOI: 10.1016/j.isci.2021.102859
    Tags: 藤原 A02
  166. Deyama, T.; Matsui, Y.; Chadani, Y.; Sekine, Y.; Doi N.,; Fujiwara, K. Transcription-translation of Escherichia coli genome within artificial cells, Chem. Commun., 2021, 57, 10367-10370,  DOI: 10.1039/d1cc04401j
    Tags: 藤原 A02
  167. Takahashi, K.; Sato, G.; Doi N.,; Fujiwara, K. A relationship between NTP and cell extract concentration for cell-free protein expression,Life, 2021, 11, 237,  DOI: 10.3390/life11030237
    Tags: 藤原 A02
  168. Furukawa, H.; Inaba,H.; Sasaki, Y.; Akiyoshi, K.; Matsuura, K.* Embedding a Membrane Protein into an Enveloped Artificial Viral Replica. RSC Chem. Biol. 2022, DOI: 10.1039/D1CB00166C
    Tags: 松浦A02

  169. Nakajima, K.; Toda, H.; Yamaguchi, K.; So, M.; Ikenaka, K.; Mochizuki, H.; Goto, Y.; Ogi, H., Half-time heat map reveals ultrasonic effects on morphology and kinetics of amyloidogenic aggregation reaction, ACS Chem. Neurosci., 2021, 12(18), 3456-3466. DOI:10.1021/acschemneuro.1c00461.

    Tags: 後藤 A02

  170. Yamaguchi, K.; Hasuo, K.; So, M.; Ikenaka, K.; Mochizuki, H.; Goto, Y., Strong acids induce amyloid fibril formation of β2-microglobulin via an anion-binding mechanism, J. Biol. Chem., 2021, 297(5), 101286. DOI:10.1016/j.jbc.2021.101286.

    Tags: 後藤 A02

  171. Bulyáki, É.; Kun, T.; Molnár, T.; Papp, A.; Micsonai, A.; Vadászi, H.; Márialigeti, B.; István Kovács, A.; Gellén, G.; Yamaguchi, K.; Lin, Y.; So, M.; Józsi, M.; Schlosser, G.; Lee, Y.-H.; Liliom, K.; Goto, Y.; Kardos, J., Pathogenic D76N variant of β2-microglobulin: Synergy of diverse effects in both the native and amyloid states, Biology, 2021, 10(11), 1197. DOI:10.3390/biology10111197.

    Tags: 後藤 A02

  172. Noji, M.; Goto, Y., 蛋白質フォールディングとミスフォールディングの統合, 生物物理, 2021, 61(6), 358-365. DOI:10.2142/biophys.61.358.

    Tags: 後藤 A02

  173. Goto, Y.; Nakajima, K.; Yamaguchi, K.; So, M.; Ikenaka, K.; Mochizuki, H.; Ogi, H., Development of HANABI, an ultrasonication-forced amyloid fibril inducer, Neurochem. Int., 2021. DOI: 10.1016/j.neuint.2021.105270. Online ahead of print. PMID: 34954259.

    Tags: 後藤 A02

  174. Umezaki. U.; Hatakenaka. M.; Onodera. K.; Mizutani. H.; Kim. S.; Nakasone. Y.; Terazima. M.; Kimura. Y.
    Effect of Hydrated Ionic Liquid on Photocycle and Dynamics of Photoactive Yellow Protein
    Molecules. 2021, 26, 4554. doi: 10.3390/molecules26154554.
    Tags:中曽根 A02
  175. Kim. S.; Nakasone. Y.; Takakado. A.; Yamazaki. Y.; Kamikubo. H.; Terazima. M .
    A unique photochromic UV-A sensor protein, Rc-PYP, interacting with the PYP-binding protein
    Phys. Chem. Chem. Phys. 2021, 23, 17813.  doi: 10.1039/d1cp02731j.
    Tags:中曽根 A02
  176. Mitsuki Tsuruta, Yui Sugitani, Naoki Sugimoto, D andDaisuke Miyoshi       
    Combined Effects of Methylated Cytosine and Molecular Crowding on the Thermodynamic Stability of DNA Duplexes     
    Int. J. Mol. Sci. , 22(2), 947 https://doi.org/10.3390/ijms22020947（2021）
    Tags:杉本A02
  177.  杉本 渉・橋本 佳樹・川内 敬子・三好 大輔            
         がん関連RNAを破壊する分子標的型光線力学療法      
    BIO Clinica    （北隆館）, 36 (5), 65-67（2021）
    Tags:杉本A02
  178. 三好大輔, 杉本直己          
    がん関連mRNAと光線力学療法  CSJカレントレビュー「生体分子と疾患」（化学同人）, 39, 75-83（2021）
    Tags:杉本A02
  179. Wataru Sugimoto, Daisuke Miyoshi, Keiko Kawauchi        
    Detection of Intracellular Reactive Oxidative Species Using the Fluorescent Probe Hydroxyphenyl Fluorescein (doi: 10.1007/978-1-0716-1258-3_18)      
    Methods Mol Biol (Live Cell Imaging), 2274, 207-215（2021）
    Tags:杉本A02
  180. 鶴田 充生・取井 猛流・杉本 渉・川内 敬子・三好 大輔        
    核酸の化学修飾と構造や相分離能の相関          
    月刊「細胞」（ニューサイエンス社）, 53 (14), 910-913（2021）
    Tags:杉本A02
  181. S.Takahashi, A. Kotar, H. Tateishi-Karimata, S. Bhowmik, Z.-F. Wang, T.-C. Chang, S, Sato, S. Takenaka, J. Plavec, and N. Sugimoto
    Chemical Modulation of DNA Replication along G-Quadruplex Based on Topology-Dependent Ligand Binding
    Am. Chem. Soc., 143, 16458-16469 (2021) [Selected as a Supplementary Cover]
    Tags:杉本A02

  182. S.Matsumoto, H. Tateishi-Karimata, T. Ohyama, and N. Sugimoto
    Effect of DNA modifications on the transition bet and non-canoncial DNA stransures in CpG islands during senescence
    RSC Adv., 11, 37205-37217 (2021)
    Tags:杉本A02

  183. W.Sugimoto, N. Kinoshita, M. Nakata, T. Ohyama, H. Tateishi-Karimata, T. Nishikata, N. Sugimoto, D. Miyoshi, and K. Kawauchi
    Intramolecular G-quadruplex-hairpin loop structure competition of a GC-rich exon region in the TMPRSS2 genChem. Commun., in 58. 38-51 (2021)
    Tags:杉本A02

  184. S.Takahashi, S. Matsumoto, P. Chilka, S. Ghosh, H. Okura, and N. Sugimoto, Dielectricity of a molecularly crowded solution accelerates NTP misincorporation during RNA-dependent RNA polymerization by T7 RNA polymerase.Sci. Rep., 12, 1149 (2022)
    Tags:杉本A02

  185. W. Sugimoto, N. Kinoshita, M. Nakata, T. Ohyama, H.Tateishi-Karimata, T. Nishikata, N. Sugimoto, D.Miyoshi, K. Kawauchi, Intramolecular G-quadruplex-hairpin loop structure competition of a GC-rich exon region in the TMPRSS2 gene. Chem. Commun. , 58, 48-51（2022）
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  186. Takeuchi K, Kofuku Y, Imai S, Ueda T, Tokunaga Y, Toyama Y, Shiraishi Y, Shimada I. Function-Related Dynamics in Multi-Spanning Helical Membrane Proteins Revealed by Solution NMR. Membranes (Basel). 2021 11(8):604. 
    Tags: 竹内A02
  187. Tokunaga Y, Takeuchi K. Role of NMR in High Ordered Structure Characterization of Monoclonal Antibodies. Int J Mol Sci. 2020 ;22(1):46.
    Tags: 竹内A02

  188. Nakagawa Y, Shen HC, Komi Y, Sugiyama S, Kurinomaru T, Tomabechi Y, Krayukhina E, Okamoto K, Yokoyama T, Shirouzu M, Uchiyama S, Inaba M, Niwa T, Sako Y, Taguchi H, Tanaka M., Amyloid conformation-dependent disaggregation in a reconstituted yeast prion system.
    Nat Chem Biol. 2022 Mar;18(3):321-331.  DOI: 10.1038/s41589-021-00951-y.
    Tags: 田中A02

  189. Hui KK, Endo R, Sawa A, Tanaka M.
    A Perspective on the Potential Involvement of Impaired Proteostasis in Neuropsychiatric Disorders. Biol Psychiatry. 2022 Feb 15;91(4):335-345. DOI: 10.1016/j.biopsych.2021.09.001.
    Tags: 田中A02

  190. Shibata. K.; Nakasone. Y.; Terazima. M.
    Selective Photoinduced Dimerization and Slow Recovery of a BLUF Domain of EB1.
    J. Phys. Chem. B. 2022, 126, 1024. doi: 10.1021/acs.jpcb.1c10100.
    Tags:中曽根 A02
  191. Tokonami. S.; Onose. M.; Nakasone. Y.; Terazima. M.
    Slow Conformational Changes of Blue Light Sensor BLUF Proteins in Milliseconds.
    J. Am. Chem. Soc. 2022, 144, 4080. doi: 10.1021/jacs.1c13121.
    Tags:中曽根 A02
  192. Nakasone. Y.; Terazima. M.
    Time-resolved diffusion reveals photoreactions of BLUF proteins with similar functional domains.
    Photochem. Photobiol. Sci. 2022, doi: 10.1007/s43630-022-00214-2. Online ahead of print.
    Tags:中曽根 A02

  193. N.Kundu, T.Sharma, S.Kaur, M.Singh, V.Kumar, U.Sharma, A.Jain, J.Shankaraswamy, D.Miyoshi, S. Saxena
    Significant structural change in human c-Myc promoter G-quadruplex upon peptide binding in potassium. RSC Adv., 12, 7594-7604 (2022)
    Tags:杉本 A02

  194. Kentarou Sakamoto, Hiroto Furukawa, Jan Vincent V. Arafiles, Miki Imanishi, Kazunori Matsuura,* Shiroh Futaki*

    Artificial nanocage formed via self-assembly of β-annulus peptide for delivering biofunctional proteins into cell interiors. Bioconjugate Chemistry, 2022, 33, 311-320. DOI: 10.1021/acs.bioconjchem.1c00534

    Tags: 松浦A02、二木A01

  195. T. Taniguchi, K. Ishizaki, D. Takagi, K. Nishimura, H. Shigemune, M. Kuramochi, Y. C. Sasaki, H. Koshima, T. Asahi
    Superelasticity of a photo-actuating chiral salicylideneamine crystal.
    Commun. Chem., Vol.5, No.4, 2022, doi: 10.1038/s42004-021-00618-8
    Tags: 倉持 A02
  196. M. Kuramochi*, Y. Dong, Y. Yang, T. Arai, R. Okada, Y. Shinkai, M. Doi, K. Aoyama, H. Sekiguchi, K. Mio, S. Tsuda, Y. C. Sasaki*
    Dynamic Motions of Ice-Binding Proteins in Living Caenorhabditis elegans Using Diffracted X-ray Blinking and Tracking
    Biochemistry and Biophysics Reports, Volume 29, 2022, 101224. doi: 10.1016/j.bbrep.2022.101224
    Tags: 倉持 A02
  197. K. T. McQuaid, S. Takahashi, L. Baumgaertner, D. J. Cardin, N. G. Paterson, J. P. Hall, N. Sugimoto, and C. J. Cardin
    Ruthenium Polypyridyl Complex Bound to a Unimolecular Chair-Form G-Quadruplex
    J. Am. Chem. Soc., 144, 5956-5964 (2022)
    Tags:杉本 A02
  198. S. Takahashi, S. Bhowmik, S. Sato, S. Takenaka, and N. Sugimoto
    Replication Control of Human Telomere G-Quadruplex DNA by G-Quadruplex Ligands Dependent on Solution Environment
    Life, 12, 553 (2022)
    Tags:杉本 A02
  199. S. Satpathi, T. Endoh, and N. Sugimoto
    Applicability of Nearest-neighbour Model for Pseudoknot RNAs
    Chem. Commun., (2022) in press
    Tags:杉本 A02
  200. S. Matsumoto, S. Takahashi, S. Bhowmik, T. Ohyama, and N. Sugimoto
    A volumetric strategy for quantitatively elucidating local hydration network around a G-quadruplex
    Anal. Chem., 94, (2022) in press
    Tags:杉本 A02
  201. R. Hatada, K. Okuwaki, Y. Mochizuki, Y. Handa, K. Fukuzawa, Y. Komeiji, Y. Okiyama, and S. Tanaka, Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease – Inhibitor N3 Complex (PDB ID: 6LU7). J. Chem. Inf. Model. 60 (2020) pp. 3593-3602.
    Tags: 田中 A02
  202. T. Dornheim, A. Cangi, K. Ramakrishna, M. Bohme, S. Tanaka, and J. Vorberger, Effective Static Approximation: A Fast and Reliable Tool for Warm-Dense Matter Theory, Phys. Rev. Lett. 125 (2020) 235001 (8 pages). https://doi.org/10.1103/PhysRevLett.125.235001
    Tags: 田中 A02
  203. D. Takaya, C. Watanabe, S. Nagase, K. Kamisaka, Y. Okiyama, H. Moriwaki, H. Yuki, T. Sato, N. Kurita, Y. Yagi, T. Takagi, N. Kawashita, K. Takaba, T. Ozawa, M. Takimoto-Kamimura, S. Tanaka, K. Fukuzawa, and T. Honma, FMODB: The World’s First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method, J. Chem. Inf. Model. 61 (2021) pp. 777-794.
    Tags: 田中 A02
  204. K. Akisawa, R. Hatada, K. Okuwaki, Y. Mochizuki, K. Fukuzawa, Y. Komeiji, and S. Tanaka, Interaction Analyses on SARS-CoV-2 Spike Protein Based on Fragment Molecular Orbital Calculations, RSC Adv. 11 (2021) pp. 3272-3279. DOI: 10.1039/d0ra09555a
    Tags: 田中 A02
  205. I. Kurisaki and S. Tanaka, Reaction Pathway Sampling and Free Energy Analyses for Multimeric Protein Complex Disassembly by Employing Hybrid Configuration Bias Monte Carlo/Molecular Dynamics Simulation, ACS Omega 6 (2021) pp. 4749-4758. DOI: 10.1021/acsomega.0c05579
    Tags: 田中 A02
  206. C. Watanabe, Y. Okiyama, S. Tanaka, K. Fukuzawa, and T. Honma, Molecular Recognition of SARS-CoV-2 Spike Glycoprotein: Quantum Chemical Hot Spot and Epitope Analyses, Chem. Sci. 12 (2021) pp. 4722-4739. DOI: 10.1039/d0sc06528e
    Tags: 田中 A02
  207. R. Hatada, K. Okuwaki, K. Akisawa, Y. Mochizuki, Y. Handa, K. Fukuzawa, Y. Komeiji, Y. Okiyama, and S. Tanaka, Statistical Interaction Analyses between SARS-CoV-2 Main Protease and Inhibitor N3 by Combining Molecular Dynamics Simulation and Fragment Molecular Orbital Calculation, Appl. Phys. Express 14 (2021) 027003 (5 pages). https://doi.org/10.35848/1882-0786/abdac6
    Tags: 田中 A02
  208. K. Sakaguchi, Y. Okiyama, and S. Tanaka, In Silico Modeling of PAX8–PPARγ Fusion Protein in Thyroid Carcinoma: Influence of Structural Perturbation by Fusion on Ligand-Binding Affinity, J. Comput. Aided Mol. Des. 35 (2021) pp. 629-642. https://doi.org/10.1007/s10822-021-00381-x
    Tags: 田中 A02
  209. Y. Okiyama, Y. Mochizuki, M. Yamanaka, and S. Tanaka, Density-Matrix Based Scheme of Basis Selection for Linear Combination of Fragment Molecular Orbitals, J. Phys. Soc. Jpn. 90 (2021) 064301 (14 pages). https://doi.org/10.7566/JPSJ.90.064301
    Tags: 田中 A02
  210. S. Tanaka, S. Tokutomi, R. Hatada, K. Okuwaki, K. Akisawa, K. Fukuzawa, Y. Komeiji, Y. Okiyama, and Y. Mochizuki, Dynamic Cooperativity of Ligand-Residue Interactions Evaluated with the Fragment Molecular Orbital Method, J. Phys. Chem. B 125 (2021) pp. 6501-6512. https://doi.org/10.1021/acs.jpcb.1c03043
    Tags: 田中 A02
  211. K. Akisawa, R. Hatada, K. Okuwaki, S. Kitahara, Y. Tachino, Y. Mochizuki, Y. Komeiji, and S. Tanaka, Fragment Molecular Orbital Based Interaction Analyses on Complexes between SARS-CoV-2 RBD Variants and ACE2, Jpn. J. Appl. Phys. 60 (2021) 090901 (5 pages). https://doi.org/10.35848/1347-4065/ac1857
    Tags: 田中 A02
  212. S. Tanaka, Appearance of Thermal Time, Found. Phys. 51 (2021) 34 (12 pages). https://doi.org/10.1007/s10701-021-00445-w
    Tags: 田中 A02
  213. A. Nishiyama, S. Tanaka, and J.A. Tuszynski, Non-Equilibrium Quantum Brain Dynamics II: Formulation in 3+1 Dimensions, Physica A 567 (2021) 125706 (23 pages). https://doi.org/10.1016/j.physa.2020.125706
    Tags: 田中 A02
  214. M. Ikejo, H. Watanabe, K. Shimamura, and S. Tanaka, Improvement of the Force Field for β-D-Glucose with Machine Learning, Molecules 26 (2021) 6691 (18 pages).
    https://doi.org/10.3390/molecules26216691
    Tags: 田中 A02
  215. I. Kurisaki and S. Tanaka, Elucidating Microscopic Events Driven by GTP Hydrolysis Reaction in the Ras-GAP System with Semi-Reactive Molecular Dynamics Simulations: The Alternative Role of a Phosphate Binding Loop for Mechanical Energy Storage, Phys. Chem. Chem. Phys. 23 (2021) pp. 26151-26164. https://doi.org/10.1039/D1CP04061H
    Tags: 田中 A02
  216. K. Okuwaki, K. Akisawa, R. Hatada, Y. Mochizuki, K. Fukuzawa, Y. Komeiji, and S. Tanaka, Collective Residue Interactions in Trimer Complexes of SARS-CoV-2 Spike Proteins Analyzed by Fragment Molecular Orbital Method, Appl. Phys. Express 15 (2022) 017001 (8 pages). https://doi.org/10.35848/1882-0786/ac4300
    Tags: 田中 A02
  217. K. Fukuzawa and S. Tanaka, Fragment Molecular Orbital Calculations for Biomolecules, Curr. Opin. Struct. Biol. 72 (2022) pp. 127-134.
    https://doi.org/10.1016/j.sbi.2021.08.010
    Tags: 田中 A02
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