Research activity information

• Xphase3d: Memory-Distributed Phase Retrieval for Reconstructing Large-Scale 3D Density Maps of Biological Macromolecules

  Wenyang Zhao, Osamu Miyashita, Miki Nakano, Florence Tama

  IEEE, Sep. 2024, 2024 IEEE International Conference on Cluster Computing (CLUSTER), 394 - 402, English

  [Refereed]

  International conference proceedings


• Structure determination using high-order spatial correlations in single-particle X-ray scattering

  Wenyang Zhao, Osamu Miyashita, Miki Nakano, Florence Tama

  Single-particle imaging using X-ray free-electron lasers (XFELs) is a promising technique for observing nanoscale biological samples under near-physiological conditions. However, as the sample's orientation in each diffraction pattern is unknown, advanced algorithms are required to reconstruct the 3D diffraction intensity volume and subsequently the sample's density model. While most approaches perform 3D reconstruction via determining the orientation of each diffraction pattern, a correlation-based approach utilizes the averaged spatial correlations of diffraction intensities over all patterns, making it well suited for processing experimental data with a poor signal-to-noise ratio of individual patterns. Here, a method is proposed to determine the 3D structure of a sample by analyzing the double, triple and quadruple spatial correlations in diffraction patterns. This ab initio method can reconstruct the basic shape of an irregular unsymmetric 3D sample without requiring any prior knowledge of the sample. The impact of background and noise on correlations is investigated and corrected to ensure the success of reconstruction under simulated experimental conditions. Additionally, the feasibility of using the correlation-based approach to process incomplete partial diffraction patterns is demonstrated. The proposed method is a variable addition to existing algorithms for 3D reconstruction and will further promote the development and adoption of XFEL single-particle imaging techniques.

  International Union of Crystallography (IUCr), Jan. 2024, IUCrJ, 11(1) (1), 92 - 108, English, International magazine

  [Refereed]

  Scientific journal


• Molecular size dependence on achievable resolution from XFEL single-particle 3D reconstruction.

  Miki Nakano, Osamu Miyashita, Florence Tama

  Single-particle analysis using x-ray free-electron lasers (XFELs) is a novel method for obtaining structural information of samples in a state close to nature. In particular, it is suitable for observing the inner structure of large biomolecules by taking advantage of the high transmittance of x-rays. However, systematic studies on the resolution achievable for large molecules are lacking. In this study, the molecular size dependence of the resolution of a three-dimensional (3D) structure resulting from XFEL single-particle reconstruction is evaluated using synthetic data. Evidently, 3D structures of larger molecules can be restored with higher detail (defined relative to the molecular sizes) than smaller ones; however, reconstruction with high absolute resolution (defined in nm-1) is challenging. Our results provide useful information for the experimental design of 3D structure reconstruction using coherent x-ray diffraction patterns of single-particles.

  Lead, Mar. 2023, Structural dynamics (Melville, N.Y.), 10(2) (2), 024101 - 024101, English, International magazine

  [Refereed]

  Scientific journal


• Three-dimensional structure determination of gold nanotriangles in solution using X-ray free-electron laser single-particle analysis

  Miki Nakano, Osamu Miyashita, Yasumasa Joti, Akihiro Suzuki, Hideyuki Mitomo, Yoshiya Niida, Ying Yang, Hirokatsu Yumoto, Takahisa Koyama, Kensuke Tono, Haruhiko Ohashi, Makina Yabashi, Tetsuya Ishikawa, Yoshitaka Bessho, Kuniharu Ijiro, Yoshinori Nishino, Florence Tama

  Lead, Jul. 2022, Optica, 9(7) (7), 776 - 784

  [Refereed]

  Scientific journal


• Parameter optimization for 3D-reconstruction from XFEL diffraction patterns based on Fourier slice matching

  Miki Nakano, Osamu Miyashita, Florence Tama

  Single-particle analysis (SPA) by X-ray free electron laser (XFEL) is a novel method that can observe biomolecules and living tissue that are difficult to crystallize in a state close to nature. To reconstruct three-dimensional (3D) molecular structure from two-dimensional (2D) XFEL diffraction patterns, we have to estimate the incident beam angle to the molecule for each pattern to assemble the 3D-diffraction intensity distribution using interpolation, and retrieve the phase information. In this study, we investigated the optimal parameter sets to assemble the 3D-diffraction intensity distribution from simulated 2D-diffraction patterns of ribosome. In particular, we examined how the parameters need to be adjusted for diffraction patterns with different binning sizes and beam intensities to obtain the highest resolution of molecular structure phase retrieved from the 3D-diffraction intensity. We found that resolution of restored molecular structure is sensitive to the interpolation parameters. Using the optimal parameter set, a linear oversampling ratio of around four is found to be sufficient for correct angle estimation and phase retrieval from the diffraction patterns of SPA by XFEL.

  Lead, Biophysical Society of Japan, 2019, Biophysics and Physicobiology, 16, 367 - 376, English, Domestic magazine

  [Refereed]

  Scientific journal


• Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution

  Miki Nakano, Osamu Miyashita, Slavica Jonic, Atsushi Tokuhisa, Florence Tama

  Lead, Jul. 2018, Journal of Synchrotron Radiation, 25(4) (4), 1010 - 1021, English

  [Refereed]

  Scientific journal


• Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL

  Miki Nakano, Osamu Miyashita, Slavica Jonic, Changyong Song, Daewoong Nam, Yasumasa Joti, Florence Tama

  The three-dimensional (3D) structural analysis of single particles using an X-ray free-electron laser (XFEL) is a new structural biology technique that enables observations of molecules that are difficult to crystallize, such as flexible biomolecular complexes and living tissue in the state close to physiological conditions. In order to restore the 3D structure from the diffraction patterns obtained by the XFEL, computational algorithms are necessary as the orientation of the incident beam with respect to the sample needs to be estimated. A program package for XFEL single-particle analysis based on theXmippsoftware package, that is commonly used for image processing in 3D cryo-electron microscopy, has been developed. The reconstruction program has been tested using diffraction patterns of an aerosol nanoparticle obtained by tomographic coherent X-ray diffraction microscopy.

  Lead, International Union of Crystallography ({IUCr}), Jul. 2017, Journal of Synchrotron Radiation, 24(4) (4), 727 - 737, English, International magazine

  [Refereed]

  Scientific journal


• Local thermodynamics of the water molecules around single- and double-stranded DNA studied by grid inhomogeneous solvation theory

  Miki Nakano, Hisae Tateishi-Karimata, Shigenori Tanaka, Florence Tama, Osamu Miyashita, Shu-ichi Nakano, Naoki Sugimoto

  Lead, Elsevier {BV}, Sep. 2016, Chemical Physics Letters, 660, 250 - 255, English

  [Refereed]

  Scientific journal


• 19pBW-9 Reconstruction of 3D structure of biomolecules from coherent diffraction patterns from XFEL

  Nakano M., Miyashita O., Jonic Slavica, Tokuhisa A., Tama Florence

  Lead, The Physical Society of Japan (JPS), 2016, Meeting Abstracts of the Physical Society of Japan, 71, 3179 - 3179, Japanese


• Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory

  Nakano, Miki, Tateishi-Karimata, Hisae, Tanaka, Shigenori, Tama, Florence, Miyashita, Osamu, Nakano, Shu-ichi, Sugimoto, Naoki

  Lead, 2015, Nucleic Acids Research, 43(21) (21), 10114 - 25, English, International magazine

  [Refereed]

  Scientific journal


• i-Motifs are more stable than G-quadruplexes in a hydrated ionic liquid

  Tateishi-Karimata, Hisae, Nakano, Miki, Pramanik, Smritimoy, Tanaka, Shigenori, Sugimoto, Naoki

  2015, Chemical Communications, 51(32) (32)

  [Refereed]

  Scientific journal


• Effects of Bridge Functions on Radial Distribution Functions of Liquid Water

  Tanaka, Shigenori, Nakano, Miki

  2015, Interdisciplinary Sciences-Computational Life Sciences, 7(2) (2)

  [Refereed]

  Scientific journal


• Comparable Stability of Hoogsteen and Watson-Crick Base Pairs in Ionic Liquid Choline Dihydrogen Phosphate

  Tateishi-Karimata, Hisae, Nakano, Miki, Sugimoto, Naoki

  2014, Scientific Reports, 4

  [Refereed]

  Scientific journal


• Classical density functional calculation of radial distribution functions of liquid water

  Tanaka, Shigenori, Nakano, Miki

  2014, Chemical Physics, 430, 18 - 22, English

  [Refereed]

  Scientific journal


• Choline Ion Interactions with DNA Atoms Explain Unique Stabilization of A-T Base Pairs in DNA Duplexes: A Microscopic View

  Nakano, Miki, Tateishi-Karimata, Hisae, Tanaka, Shigenori, Sugimoto, Naoki

  Lead, 2014, Journal of Physical Chemistry B, 118(2) (2), 379 - 389

  [Refereed]

  Scientific journal


• Affinity of Molecular Ions for DNA Structures Is Determined by Solvent-Accessible Surface Area

  Nakano, Miki, Tateishi-Karimata, Hisae, Tanaka, Shigenori, Sugimoto, Naoki

  Lead, 2014, Journal of Physical Chemistry B, 118(32) (32), 9583 - 9594

  [Refereed]

  Scientific journal


• 3P119 Analysis for the effect of choline ions on the stability of DNA base pairs using molecular dynamics simulation(05A. Nucleic acid: Structure & Property,Poster)

  Nakano Miki, Tateishi-Karimata Hisae, Sugimoto Naoki

  Lead, The Biophysical Society of Japan General Incorporated Association, 2013, Seibutsu Butsuri, 53(1) (1), S231, English


• Triplet correlations and bridge functions in classical density functional theory for liquid water

  Tanaka, Shigenori, Nakano, Miki

  2013, Chemical Physics Letters, 572, 38 - 43, English

  [Refereed]

  Scientific journal


• Study of the aggregation mechanism of polyglutamine peptides using replica exchange molecular dynamics simulations

  Nakano, Miki, Ebina, Kuniyoshi, Tanaka, Shigenori

  Lead, 2013, Journal of Molecular Modeling, 19(4) (4), 1627 - 1639

  [Refereed]

  Scientific journal


• Molecular mechanics and all-electron fragment molecular orbital calculations on mutated polyglutamine peptides

  Van Schouwen, Bryan M. B., Nakano, Miki, Watanabe, Hirofumi, Tanaka, Shigenori, Gordon, Heather L., Rothstein, Stuart M.

  2010, Journal of Molecular Structure-Theochem, 944(1-3) (1-3), 12 - 20

  [Refereed]

  Scientific journal


• Comparative Characterization of Short Monomeric Polyglutamine Peptides by Replica Exchange Molecular Dynamics Simulation

  Nakano, Miki, Watanabe, Hirofumi, Rothstein, Stuart M., Tanaka, Shigenori

  Lead, 2010, Journal of Physical Chemistry B, 114(20) (20), 10234 - 10234

  [Refereed]

  Scientific journal


• 1P-055 Characterization of monomeric polyglutamine peptides by replica exchange molecular dynamics simulation(Protein:Property, The 47th Annual Meeting of the Biophysical Society of Japan)

  Nakano Miki, Watanabe Hirofumi, Tanaka Shigenori

  Lead, The Biophysical Society of Japan General Incorporated Association, 2009, Seibutsu Butsuri, 49, S71 - S72, English


• Mutation Effects on Structural Stability of Polyglutamine Peptides by Molecular Dynamics Simulation

  Nakano, Miki, Watanabe, Hirofumi, Starikov, E. B., Rothstein, Stuart M., Tanaka, Shigenori

  Lead, 2009, Interdisciplinary Sciences-Computational Life Sciences, 1(1) (1), 21 - 29

  [Refereed]

  Scientific journal


• Molecular dynamics simulation study on the structural stabilities of polyglutamine peptides

  Ogawa, Hajime, Nakano, Miki, Watanabe, Hirofumi, Starikov, E. B., Rothstein, Stuart M., Tanaka, Shigenori

  2008, Computational Biology and Chemistry, 32(2) (2), 102 - 110

  [Refereed]

  Scientific journal

• Protocol for three-dimensional structure reconstruction using simulated XFEL coherent diffraction data

  Nakano Miki, Miyashita Osamu, Jonic Slavica, Tokuhisa Atsushi, Tama Florence

  The Physical Society of Japan, 2018, Meeting Abstracts of the Physical Society of Japan, 73(0) (0), 3078 - 3078, Japanese

• 新しい高校物理の教科書

  山本, 明利, 左巻, 健男

  Joint work, 第5章 波うつ世界, 講談社, Feb. 2006, Japanese, ISBN: 4062575094

• 日本蛋白質科学会


• The Biophysics Society (US)


• 日本放射光学会


• 生物物理学会

• XFEL単粒子回折画像処理と三次元生体分子構造の復元

  中野 美紀

  日本学術振興会, 科学研究費助成事業 若手研究, 若手研究, 国立研究開発法人理化学研究所, 01 Apr. 2018 - 31 Mar. 2022

  X線自由電子レーザー（XFEL）による単粒子立体構造解析は、膜タンパク質や巨大複合体など、結晶化が難しい生体分子や生体組織を自然に近い状態で観察できる新しい構造生物学的手法である。 実空間で高い解像度を持つ分子構造を復元するためには、十分な回折強度を持つ回折画像が必要である。しかしXFELの強いビームを用いても、単粒子の生体分子から得られる回折強度は極めて弱く、回折画像のS/N比は極めて小さい。通常、S/N比を高めるため、実験で得られた回折像は、解析の前にbinningやcroppingなどの前処理が行われる。しかし、検出器上で複数のピクセルをまとめるbinning は、波数空間内での解像度を粗くすることに相当し、まとめられたピクセル内の詳細情報が失われることになる。また、二次元回折像を三次元回折強度分布に組み立てる際には、波数空間内での回折強度を補間する必要があるが、binningによる解像度の変化は、この補間パラメーターの調整も必要とする。 我々は、シミュレーションにより作成したリボソームの二次元回折像から三次元回折強度分布を組み立てるための最適なパラメーターセットの調査を行った。その結果、位相回復法によって復元された分子構造の解像度は、補間パラメーターには敏感であるが、binning ステップサイズによる影響は小さいことが判明した。波数空間内での三次元回折強度分布構築に最適なパラメーターセットを使用すると、binningステップサイズは線形オーバーサンプリング比4に相当するサイズで十分であることを示した。