Masayoshi Nakasako

Summary

Affiliation: Keio University
Country: Japan

Publications

  1. ncbi request reprint Structural basis of the LOV1 dimerization of Arabidopsis phototropins 1 and 2
    Masayoshi Nakasako
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Kanagawa 223 8522, Japan
    J Mol Biol 381:718-33. 2008
  2. pmc Crystallization and preliminary X-ray diffraction experiments of arylmalonate decarboxylase from Alcaligenes bronchisepticus
    Masayoshi Nakasako
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Kanagawa 223 8522, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 64:610-3. 2008
  3. pmc Crystallization and preliminary X-ray diffraction analysis [correction of anaylsis] of the LOV1 domains of phototropin 1 and 2 from Arabidopsis thaliana
    Masayoshi Nakasako
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Kanagawa 223 8522, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 64:617-21. 2008
  4. ncbi request reprint Redox-dependent domain rearrangement of protein disulfide isomerase from a thermophilic fungus
    Masayoshi Nakasako
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kouho ku, Yokohama 223 8522, Japan
    Biochemistry 49:6953-62. 2010
  5. ncbi request reprint Conformational dynamics of complementarity-determining region H3 of an anti-dansyl Fv fragment in the presence of its hapten
    Masayoshi Nakasako
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, Kanagawa 223 8522, Japan
    J Mol Biol 351:627-40. 2005
  6. ncbi request reprint Quaternary structure of LOV-domain containing polypeptide of Arabidopsis FKF1 protein
    Masayoshi Nakasako
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Kanagawa 223 8522, Japan
    FEBS Lett 579:1067-71. 2005
  7. ncbi request reprint Light-induced global structural changes in phytochrome A regulating photomorphogenesis in plants
    Masayoshi Nakasako
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Kanagawa 223 8522, Japan
    FEBS J 272:603-12. 2005
  8. ncbi request reprint Light-induced structural changes of LOV domain-containing polypeptides from Arabidopsis phototropin 1 and 2 studied by small-angle X-ray scattering
    Masayoshi Nakasako
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1, Hiyoshi, Kohoku Ku, Kanagawa 223 8522, Japan
    Biochemistry 43:14881-90. 2004
  9. pmc Water-protein interactions from high-resolution protein crystallography
    Masayoshi Nakasako
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, Kanagawa 223 8522, Japan
    Philos Trans R Soc Lond B Biol Sci 359:1191-204; discussion 1204-6. 2004
  10. doi request reprint Light-induced movement of the LOV2 domain in an Asp720Asn mutant LOV2-kinase fragment of Arabidopsis phototropin 2
    Yuki Takayama
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1Hiyoshi, Kohoku Ku, Kanagawa 223 8522, Japan
    Biochemistry 50:1174-83. 2011

Collaborators

Detail Information

Publications25

  1. ncbi request reprint Structural basis of the LOV1 dimerization of Arabidopsis phototropins 1 and 2
    Masayoshi Nakasako
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Kanagawa 223 8522, Japan
    J Mol Biol 381:718-33. 2008
    ..The present results also provide clues to understanding structural basis in dimeric interactions of Per-ARNT-Sim protein modules in cellular signaling...
  2. pmc Crystallization and preliminary X-ray diffraction experiments of arylmalonate decarboxylase from Alcaligenes bronchisepticus
    Masayoshi Nakasako
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Kanagawa 223 8522, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 64:610-3. 2008
    ..Small-angle X-ray scattering revealed that the enzyme exists as a monomer in solution. Thus, the assembly of molecules in the asymmetric unit was likely to have been induced during the crystallization process...
  3. pmc Crystallization and preliminary X-ray diffraction analysis [correction of anaylsis] of the LOV1 domains of phototropin 1 and 2 from Arabidopsis thaliana
    Masayoshi Nakasako
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Kanagawa 223 8522, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 64:617-21. 2008
    ..5, b = 66.5, c = 56.7 A, beta = 92.4 degrees , and diffracted X-rays to beyond 2.0 A resolution. In both crystals, two LOV1 domains occupied the crystallographic asymmetric unit...
  4. ncbi request reprint Redox-dependent domain rearrangement of protein disulfide isomerase from a thermophilic fungus
    Masayoshi Nakasako
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kouho ku, Yokohama 223 8522, Japan
    Biochemistry 49:6953-62. 2010
    ..On the basis of the results presented here, we propose a mechanism explaining the observed redox-dependent conformational and solvation changes of PDI...
  5. ncbi request reprint Conformational dynamics of complementarity-determining region H3 of an anti-dansyl Fv fragment in the presence of its hapten
    Masayoshi Nakasako
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, Kanagawa 223 8522, Japan
    J Mol Biol 351:627-40. 2005
    ..The conformational dynamics of H3 in recognizing and binding the hapten molecule are discussed on the basis of the structural information from the present and previous studies...
  6. ncbi request reprint Quaternary structure of LOV-domain containing polypeptide of Arabidopsis FKF1 protein
    Masayoshi Nakasako
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Kanagawa 223 8522, Japan
    FEBS Lett 579:1067-71. 2005
    ..Based on the homologies in the amino-acid sequences and the scattering profiles, these results are discussed in connection with the structures and function of LOV domains of phototropin...
  7. ncbi request reprint Light-induced global structural changes in phytochrome A regulating photomorphogenesis in plants
    Masayoshi Nakasako
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Kanagawa 223 8522, Japan
    FEBS J 272:603-12. 2005
    ..Red-light-induced structural changes in Pfr were reversible, mostly due to thermal relaxation processes...
  8. ncbi request reprint Light-induced structural changes of LOV domain-containing polypeptides from Arabidopsis phototropin 1 and 2 studied by small-angle X-ray scattering
    Masayoshi Nakasako
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1, Hiyoshi, Kohoku Ku, Kanagawa 223 8522, Japan
    Biochemistry 43:14881-90. 2004
    ..On the basis of the results, the interdomain interactions in phototropin are discussed...
  9. pmc Water-protein interactions from high-resolution protein crystallography
    Masayoshi Nakasako
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, Kanagawa 223 8522, Japan
    Philos Trans R Soc Lond B Biol Sci 359:1191-204; discussion 1204-6. 2004
    ....
  10. doi request reprint Light-induced movement of the LOV2 domain in an Asp720Asn mutant LOV2-kinase fragment of Arabidopsis phototropin 2
    Yuki Takayama
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1Hiyoshi, Kohoku Ku, Kanagawa 223 8522, Japan
    Biochemistry 50:1174-83. 2011
    ....
  11. ncbi request reprint Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc
    Takashi Kumasaka
    Department of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa 226 8501, Japan
    J Biol Chem 282:37103-11. 2007
    ....
  12. doi request reprint Structural basis for inverting the enantioselectivity of arylmalonate decarboxylase revealed by the structural analysis of the Gly74Cys/Cys188Ser mutant in the liganded form
    Rika Obata
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, Kanagawa 223 8522, Japan
    Biochemistry 49:1963-9. 2010
    ..These results may provide an effective strategy for the rational design to invert the enantioselectivity of enzymes...
  13. ncbi request reprint Prediction of hydration structures around hydrophilic surfaces of proteins by using the empirical hydration distribution functions from a database analysis
    Daisuke Matsuoka
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, Kanagawa 223 8522, Japan
    J Phys Chem B 114:4652-63. 2010
    ..In addition, it will be used to predict hydration structures of proteins available at resolutions insufficient to identify water molecules...
  14. ncbi request reprint Humidity-controlled preparation of frozen-hydrated biological samples for cryogenic coherent x-ray diffraction microscopy
    Yuki Takayama
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kanagawa 223 8522, Japan
    Rev Sci Instrum 83:054301. 2012
    ..Taking the performance of the system and the quality of the sample, the system was suitable to prepare frozen-hydrated biological samples for cryogenic CXDM experiments...
  15. doi request reprint KOTOBUKI-1 apparatus for cryogenic coherent X-ray diffraction imaging
    Masayoshi Nakasako
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama 223 8522, Japan
    Rev Sci Instrum 84:093705. 2013
    ..Recently, it has been applied for single-shot diffraction data collection of non-crystalline particles with dimensions of sub-μm using X-ray free electron laser at BL3 of SACLA. ..
  16. ncbi request reprint Enzymatic characterization of scytalone dehydratase Val75Met variant found in melanin biosynthesis dehydratase inhibitor (MBI-D) resistant strains of the rice blast fungus
    Naoki Yamada
    Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa, Japan
    Biosci Biotechnol Biochem 68:615-21. 2004
    ..Based on the results, here we propose possible mechanisms of the carpropamid-resistance of the variant enzyme in retaining the normal enzymatic activity...
  17. ncbi request reprint Data processing software suite SITENNO for coherent X-ray diffraction imaging using the X-ray free-electron laser SACLA
    Yuki Sekiguchi
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama 223 8522, Japan
    J Synchrotron Radiat 21:600-12. 2014
    ..Using the SITENNO suite, it is possible to conduct experiments with data processing immediately after the data collection, and to characterize the size distribution and internal structures of the non-crystalline particles. ..
  18. doi request reprint A few low-frequency normal modes predominantly contribute to conformational responses of hen egg white lysozyme in the tetragonal crystal to variations of molecular packing controlled by environmental humidity
    Yuki Takayama
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kanagawa 223 8522, Japan
    Biophys Chem 159:237-46. 2011
    ..These findings suggest that humidity-controlled X-ray crystallography is an effective tool to investigate the responses of inherent intramolecular motions of proteins to external perturbations...
  19. ncbi request reprint Probability distributions of hydration water molecules around polar protein atoms obtained by a database analysis
    Daisuke Matsuoka
    Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223 8522, Japan
    J Phys Chem B 113:11274-92. 2009
    ..These probability distributions are probably one of fundamental data to better understand the roles of hydration water molecules in the folding process and the stability of proteins in solution...
  20. ncbi request reprint Application of a real-space three-dimensional image reconstruction method in the structural analysis of noncrystalline biological macromolecules enveloped by water in coherent x-ray diffraction microscopy
    Wataru Kodama
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, Kanagawa 223 8522, Japan
    Phys Rev E Stat Nonlin Soft Matter Phys 84:021902. 2011
    ..In particular, we examined the influence of Poisson noise in diffraction patterns on the reconstructed three-dimensional electron density in the proposed protocol...
  21. ncbi request reprint Three-dimensional structure determination protocol for noncrystalline biomolecules using x-ray free-electron laser diffraction imaging
    Tomotaka Oroguchi
    Department of Physics, Faculty of Science and Technology, Keio University, 3 14 1 Hiyoshi, Yokohama, Kanagawa 223 8522, Japan
    Phys Rev E Stat Nonlin Soft Matter Phys 87:022712. 2013
    ..8 nm when an x-ray beam of 10(16) photons/500×500 nm(2)/pulse is available...
  22. ncbi request reprint Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: on the correlation between crystal water sites, solvent density, and solvent dipole
    Junichi Higo
    Laboratory of Bioinformatics, School of Life Science, Tokyo University of Pharmacy and Life Science and BIRD, JST Japan Science and Technology Corporation, 1432 1 Horinouchi, Hachioji, Tokyo, 192 0392, Japan
    J Comput Chem 23:1323-36. 2002
    ..The present work may provide a new approach combining computational and the experimental studies to understand protein hydration...
  23. ncbi request reprint Roles of hydration water molecules in molecular packing of the killer toxin from Pichia farinosa in its crystalline state investigated by cryogenic X-ray crystallography
    Masayoshi Nakasako
    Precursory Research for Embryonic Science and Technology, Japan Science and Technology Corporation and Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Bunkyo ku, Tokyo 113 0032, Japan
    Biophys Chem 95:211-25. 2002
    ..The present analysis may provide a way to analyze the crystal contact and molecular recognition in macromolecules in aqueous solution...
  24. ncbi request reprint Nonlinear temperature dependence of the crystal structure of lysozyme: correlation between coordinate shifts and thermal factors
    Yasumasa Joti
    Department of Science, Kyoto University, Kitashirakawa, Sakyo ku, Japan
    Acta Crystallogr D Biol Crystallogr 58:1421-32. 2002
    ..Possible causes for the dynamic transition are discussed with respect to the crystal packing and physicochemical properties of crystalline water...
  25. ncbi request reprint Crystallization of scytalone dehydratase F162A mutant in the unligated state and a preliminary X-ray diffraction study at 37 K
    Takayuki Motoyama
    RIKEN The Institute of Physical and Chemical Research, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
    Acta Crystallogr D Biol Crystallogr 58:148-50. 2002
    ..62 A, beta = 120.02 degrees at 37 K. The calculated V(M) value was acceptable when a trimer of the mutant enzyme occupied a crystallographic asymmetric unit. The resolution limit was extended to 1.45 A at BL41XU of SPring-8 at 37 K...