MIYASHITA Naoyuki

Researcher Information

URL

http://www2.miyashita-lab.net

Research funding number

• 20452162

J-Global ID

• 201501041956423540

Research Interests

• Artificial Intelligence for biophysics   シミュレーション   Molecular mechanism of Alzheimer's disease   replica-exchange   混合膜   ラフト   

Research Areas

• Informatics / Biological, health, and medical informatics

Academic & Professional Experience

• 2018/04 - Today  University of Electro-Communicatins基盤理工学専攻Visiting Associate Professor
• 2018/04 - Today  RIKEN Center for Biosystems Dynamics ResearchVisiting Scientist
• 2017/04 - Today  KINDAI UniversityBiology Oriented Science & TechnologyAssociate Professor
• 2016/04 - Today  Kindai University生物理工学研究科 生体システム工学専攻准教授
• 2015/08 - Today  RIKEN AICSVisiting Scientists
• 2015/04 - 2018/03  RIKEN QBiCVisiting Scientist
• 2015/04 - 2017/03  KINDAI UniversityBiology Oriented Science & TechnologyAssociate Professor
• 2011/04 - 2015/03  RIKENAICSResearch Scientist
• 2011/04 - 2015/03  RIKENQBiCResearch Scientist
• 2013/07 - 2013/07  Kobe University理学研究科非常勤講師
• 2011/04 - 2013/03  RIKENISLiMResearch Scientist
• 2007/12 - 2011/03  RIKENISLiMResearch Scientist
• 2007/04 - 2007/11  GIFU UniversityCEIDAssistant Professor
• 2005/04 - 2007/03  BOSTON UniversityChemistry DepartmentResearch Associate
• 2003/04 - 2005/03  The University of TokyoIMCBPost Doctoral fellow
• 2001/06 - 2003/02  岡崎国立共同研究機構RA

Education

• 1999/04 - 2003/03  The Graduage University for Advanced Study  数物科学研究科  機能分子科学専攻
• 1997/04 - 1999/03  University of Electro-Communications  Department of Electro-Communications  Advanced physics and chemistry
• 1992/04 - 1997/03  University of Electro-Communications  Department of Electro-Communications  Applied physics and chemistry

Association Memberships

• 日本ゲノム編集学会   THE PHYSICAL SOCIETY OF JAPAN   THE MOLECULAR BIOLOGY SOCIETY OF JAPAN   THE BIOPHYSICAL SOCIETY   The Chemical Society of America   THE BIOPHYSICAL SOCIETY OF JAPAN   理論化学会   日本蛋白質質科学会   

Published Papers

• Interaction between PET tracer and the specific residues around the gate of the open form of Monoamine Oxidase B (MAO-B)

  M. Ottawa; N. Miyashita

  Journal of Physics: Conference Series 2207 012025  2022/03 [Refereed][Invited]
  
• Simulation study of the function of domain swapping in the HSP90 chaperone cycle

  L. Matsukura; N. Miyashita

  Journal of Physics: Conference Series 2207 012024  2022/03 [Refereed][Invited]
  
• Simulation Study of the Stability of Heat Shock Protein 90 (HSP90) and Co-chaperone p23 Complex

  Lisa MATSUKURA; Naoyuki MIYASHITA

  Journal of Computer Chemistry, Japan Society of Computer Chemistry Japan 20 (3) 94 - 96 1347-1767 2021/11 [Refereed][Invited]
  
• 新規ゲノム編集ツールTiDを用いたヒト細胞でのゲノム編集

  和田 直樹; 村上 愛美; 丸井 和也; 宮下 尚之; 刑部 祐里子; 刑部 敬史

  日本生物工学会大会講演要旨集 (公社)日本生物工学会 2021年 103 - 103 2021/10
• Mutual information analysis of the dynamic correlation between side chains in proteins

  Naoyuki Miyashita; Yasushige Yonezawa

  The Journal of Chemical Physics AIP Publishing 155 (4) 044107 - 044107 0021-9606 2021/07 [Refereed]
  
• Genome editing in mammalian cells using the CRISPR type I-D nuclease

  Keishi Osakabe; Naoki Wada; Emi Murakami; Naoyuki Miyashita; Yuriko Osakabe

  Nucleic Acids Research Oxford University Press (OUP) 49 (11) 6347 - 6363 0305-1048 2021/06 [Refereed]
   

  Adoption of CRISPR–Cas systems, such as CRISPR–Cas9 and CRISPR–Cas12a, has revolutionized genome engineering in recent years; however, application of genome editing with CRISPR type I—the most abundant CRISPR system in bacteria—remains less developed. Type I systems, such as type I-E, and I-F, comprise the CRISPR-associated complex for antiviral defense (‘Cascade’: Cas5, Cas6, Cas7, Cas8 and the small subunit) and Cas3, which degrades the target DNA; in contrast, for the sub-type CRISPR–Cas type I-D, which lacks a typical Cas3 nuclease in its CRISPR locus, the mechanism of target DNA degradation remains unknown. Here, we found that Cas10d is a functional nuclease in the type I-D system, performing the role played by Cas3 in other CRISPR–Cas type I systems. The type I-D system can be used for targeted mutagenesis of genomic DNA in human cells, directing both bi-directional long-range deletions and short insertions/deletions. Our findings suggest the CRISPR–Cas type I-D system as a unique effector pathway in CRISPR that can be repurposed for genome engineering in eukaryotic cells.
• Medium-firm drug-candidate library of cryptand-like structures on T7 phage: Design and selection of strong binder for Hsp90

  Kazuto Mochizuki; Lisa Matsukura; Yuji Ito; Naoyuki Miyashita; Masumi Taki

  Organic & Biomolecular Chemistry 19 (1) 146 - 150 2021/01 [Refereed]
   

  We designed and synthesized a medium-firm drug-candidate library of cryptand-like structures possessing a randomized peptide linker on the bacteriophage T7. From the macrocyclic library with a 109 diversity, we obtained a binder toward a cancer-related protein (Hsp90) with an antibody-like strong affinity (KD = 62 nM) and the binding was driven by the enthalpy. The selected supramolecular ligand inhibited Hsp90 activity by site-specific binding outside of the well-known ATP-binding pocket on the N-terminal domain (NTD).
• Structural and Functional Basis for LILRB Immune Checkpoint Receptor Recognition of HLA-G isoforms

  黒木, 喜美子; 松原, 永季; 神田, 諒; 宮下, 尚之; 白石, 充典; 福永, 裕子; 上敷領, 淳; 福永, 淳; 福原, 秀雄; 廣瀬, 薫; Hunt, Joan S; 杉田, 有治; 喜多, 俊介; 尾瀬, 農之; 前仲, 勝実

  福山大学薬学部研究年報 = Annual report of the Faculty of Pharmacy & Pharmaceutical Sciences, Fukuyama University 福山大学薬学部 38 35 - 36 0288-724X 2020/12
• Structural and Functional Basis for LILRB Immune Checkpoint Receptor Recognition of HLA-G Isoforms.

  Kimiko Kuroki; Haruki Matsubara; Ryo Kanda; Naoyuki Miyashita; Mitsunori Shiroishi; Yuko Fukunaga; Jun Kamishikiryo; Atsushi Fukunaga; Hideo Fukuhara; Kaoru Hirose; Joan S Hunt; Yuji Sugita; Shunsuke Kita; Toyoyuki Ose; Katsumi Maenaka

  Journal of immunology (Baltimore, Md. : 1950) 203 (12) 3386 - 3394 2019/12 [Refereed]
   

  Human leukocyte Ig-like receptors (LILR) LILRB1 and LILRB2 are immune checkpoint receptors that regulate a wide range of physiological responses by binding to diverse ligands, including HLA-G. HLA-G is exclusively expressed in the placenta, some immunoregulatory cells, and tumors and has several unique isoforms. However, the recognition of HLA-G isoforms by LILRs is poorly understood. In this study, we characterized LILR binding to the β2-microglobulin (β2m)-free HLA-G1 isoform, which is synthesized by placental trophoblast cells and tends to dimerize and multimerize. The multimerized β2m-free HLA-G1 dimer lacked detectable affinity for LILRB1, but bound strongly to LILRB2. We also determined the crystal structure of the LILRB1 and HLA-G1 complex, which adopted the typical structure of a classical HLA class I complex. LILRB1 exhibits flexible binding modes with the α3 domain, but maintains tight contacts with β2m, thus accounting for β2m-dependent binding. Notably, both LILRB1 and B2 are oriented at suitable angles to permit efficient signaling upon complex formation with HLA-G1 dimers. These structural and functional features of ligand recognition by LILRs provide novel insights into their important roles in the biological regulations.
• On-the-fly analysis of molecular dynamics simulation trajectories of proteins using the Bayesian inference method

  Naoyuki Miyashita; Yasushige Yonezawa

  JOURNAL OF CHEMICAL PHYSICS AMER INST PHYSICS 147 (12) 124108-1 - 124108-8 0021-9606 2017/09 [Refereed]
   

  Robust and reliable analyses of long trajectories from molecular dynamics simulations are important for investigations of functions and mechanisms of proteins. Structural fitting is necessary for various analyses of protein dynamics, thus removing time-dependent translational and rotational movements. However, the fitting is often difficult for highly flexible molecules. Thus, to address the issues, we proposed a fitting algorithm that uses the Bayesian inference method in combination with rotational fitting-weight improvements, and the well-studied globular protein systems trpcage and lysozyme were used for investigations. The present method clearly identified rigid core regions that fluctuate less than other regions and also separated core regions from highly fluctuating regions with greater accuracy than conventional methods. Our method also provided simultaneous variance-covariance matrix elements composed of atomic coordinates, allowing us to perform principle component analysis and prepare domain cross-correlation map during molecular dynamics simulations in an on-the-fly manner. Published by AIP Publishing.
• Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

  Takaharu Mori; Naoyuki Miyashita; Wonpil Im; Michael Feig; Yuji Sugita

  BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES ELSEVIER SCIENCE BV 1858 (7) 1635 - 1651 0005-2736 2016/07 [Refereed][Invited]
   

  This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. (C) 2016 The Authors. Published by Elsevier B.V.
• 21pBF-8 The Dimerization mechanism of Amyloid precursor protein (APP) is affected by Cholesterol

  Miyashita N.; Ogushi F.; Sugita Y.

  Meeting Abstracts of the Physical Society of Japan The Physical Society of Japan (JPS) 71 3234 - 3234 2189-079X 2016
• REIN: Replica-Exchange INterface for Simulating Protein Dynamics and Function

  Naoyuki Miyashita; Suyong Re; Yuji Sugita

  INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY WILEY 115 (5) 325 - 332 0020-7608 2015/03 [Refereed]
   

  Replica-exchange molecular dynamics (REMD) method is one of the enhanced conformational sampling algorithms widely applied in computational biophysics and biochemistry. In the method, molecular dynamics (MD) simulations for multiple replicas of a target system are performed simultaneously and independently. Every few steps, temperatures or other parameters are exchanged between a pair of replicas according to the modified Metropolis criteria. Replica-Exchange INterface (REIN) is interface software for REMD simulations. It utilizes existing MD software without modification and performs the exchanges of replicas. In this article, we introduce the software design of REIN and demonstrate its applicability through benchmark simulations of alanine pentapeptide in explicit water, as well as the free-energy analysis of N-glycan and Tom20-presequence complex in solution. (c) 2014 Wiley Periodicals, Inc.
• Multidimensional Umbrella Sampling and Replica-Exchange Molecular Dynamics Simulations for Structure Prediction of Transmembrane Helix Dimers

  Pai-Chi Li; Naoyuki Miyashita; Wonpil Im; Satoshi Ishido; Yuji Sugita

  JOURNAL OF COMPUTATIONAL CHEMISTRY WILEY-BLACKWELL 35 (4) 300 - 308 0192-8651 2014/02 [Refereed]
   

  Structural information of a transmembrane (TM) helix dimer is useful in understanding molecular mechanisms of important biological phenomena such as signal transduction across the cell membrane. Here, we describe an umbrella sampling (US) scheme for predicting the structure of a TM helix dimer in implicit membrane using the interhelical crossing angle and the TM-TM relative rotation angles as the reaction coordinates. This scheme conducts an efficient conformational search on TM-TM contact interfaces, and its robustness is tested by predicting the structures of glycophorin A (GpA) and receptor tyrosine kinase EphA1 (EphA1) TM dimers. The nuclear magnetic resonance (NMR) structures of both proteins correspond to the global free-energy minimum states in their free-energy landscapes. In addition, using the landscape of GpA as a reference, we also examine the protocols of temperature replica-exchange molecular dynamics (REMD) simulations for structure prediction of TM helix dimers in implicit membrane. A wide temperature range in REMD simulations, for example, 250-1000 K, is required to efficiently obtain a free-energy landscape consistent with the US simulations. The interhelical crossing angle and the TM-TM relative rotation angles can be used as reaction coordinates in multidimensional US and be good measures for conformational sampling of REMD simulations. (C) 2013 Wiley Periodicals, Inc.
• 研究室だより 理化学研究所 杉田理論分子科学研究室

  宮下 尚之; 李 秀栄; 杉田 有治

  アンサンブル : 分子シミュレーション研究会会誌 分子シミュレーション研究会 16 (1) 65 - 68 1884-6750 2014/01 [Invited]
  
• 1P211 Cholesterols affect to the association of the transmembrane region of Amyloid Precursor Protein in the raft(13B. Biological & Artificial membrane: Dynamics,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

  Miyashita Naoyuki; Ogushi Fumiko; Sugita Yuji

  Seibutsu Butsuri The Biophysical Society of Japan General Incorporated Association 54 (1) S176  2014
• 1P100 Comparison of the predicted structure of the FGFR3 transmembrane domain by enhanced sampling simulations with experimental results(03. Membrane proteins,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

  Kashihara Yumi; Miyashita Naoyuki; Li Pai-Chi; Sugita Yuji

  Seibutsu Butsuri The Biophysical Society of Japan General Incorporated Association 54 (1) S157  2014
• Energetics of the presequence-binding poses in mitochondrial protein import through Tom20

  Yasuaki Komuro; Naoyuki Miyashita; Takaharu Mori; Eiro Muneyuki; Takashi Saitoh; Daisuke Kohda; Yuji Sugita

  Journal of Physical Chemistry B American Chemical Society 117 (10) 2864 - 2871 1520-5207 2013/03 [Refereed]
   

  Tom20 is located at the outer membrane of mitochondria and functions as a receptor for the N-terminal presequence of mitochondrial-precursor proteins. Recently, three atomic structures of the Tom20-presequence complex were determined using X-ray crystallography and classified into A-, M-, and Y-poses in terms of their presequence-binding modes. Combined with biochemical and NMR data, a dynamic-equilibrium model between the three poses has been proposed. To investigate this mechanism in further detail, we performed all-atom molecular dynamics (MD) simulations and replica-exchange MD (REMD) simulations of the Tom20-presequence complex in explicit water. In the REMD simulations, one major distribution and another minor one were observed in the converged free-energy landscape at 300 K. In the major distribution, structures similar to A- and M-poses exist, whereas those similar to Y-pose are located in the minor one, suggesting that A-pose in solution is more stable than Y-pose. A k-means clustering algorithm revealed a new pose not yet obtained by X-ray crystallography. This structure has double salt bridges between Arg14′ in the presequence and Glu78 or Glu79 in Tom20 and can explain the binding affinity of the complex in previous pull-down assay experiments. Structural clustering and analyses of contacts between Tom20 and the presequence suggest smooth conformational changes from Y- to A-poses through low activation barriers. M-pose lies between Y- and A-poses as a metastable state. The REMD simulations thus provide insights into the energetics of the multiple-binding forms and help to detail the progressive conformational states in the dynamic-equilibrium model based on the experimental data. © 2013 American Chemical Society.
• Free Energy Analysis on the Tom20-Presequence Complex in Solution for Understanding a Dynamic-Equilibrium Model

  Komuro Yasuaki; Miyashita Naoyuki; Mori Takaharu; Muneyuki Eiro; Saitoh Takashi; Kohda Daisuke; Sugita Yuji

  BIOPHYSICAL JOURNAL 104 (2) 665A  0006-3495 2013/01 [Refereed]
  
• 3P112 Interaction between cholesterol and transmembrane region of Amyloid Precursor Protein(03. Membrane proteins,Poster)

  Miyashita Naoyuki; Ogushi Fumiko; Sugita Yuji

  Seibutsu Butsuri The Biophysical Society of Japan General Incorporated Association 53 (1) S230  2013
• Recent Applications of Replica-Exchange Molecular Dynamics Simulations of Biomolecules

  Yuji Sugita; Naoyuki Miyashita; Pai-Chi Li; Takao Yoda; Yuko Okamoto

  Current Physical Chemistry 2 (4) 401 - 412 2012/12 [Refereed]
  
• Effect of Bisecting GlcNAc and Core Fucosylation on Conformational Properties of Biantennary Complex-Type N-Glycans in Solution

  Wataru Nishima; Naoyuki Miyashita; Yoshiki Yamaguchi; Yuji Sugita; Suyong Re

  JOURNAL OF PHYSICAL CHEMISTRY B AMER CHEMICAL SOC 116 (29) 8504 - 8512 1520-6106 2012/07 [Refereed]
   

  The introduction of bisecting GlcNAc and core fucosylation in N-glycans is essential for fine functional regulation of glycoproteins. In this paper, the effect of these modifications on the conformational properties Of N-glycans is examined at the atomic level by performing replica exchange molecular dynamics (REMD) simulations. We simulate four biantennary complex type N-glycans, namely, unmodified, two single substituted with either bisecting GlcNAc or core fucose, and disubstituted forms. By using REMD as an enhanced sampling technique, five distinct conformers in solution, each of which is characterized by its local orientation of the Man alpha 1-6Man glycosidic linkage, are observed for all four N-glycans. The chemical modifications significantly change their conformational equilibria. The number of major conformers is reduced from five to two and from five to four upon the introduction of bisecting GlcNAc and core fucosylation; respectively, The population change is attributed to specific inter residue hydrogen bonds, including water mediated Ones. The experimental NMR data, including nuclear Overhauser enhancement and scalar J-coupling constant's, are well reproduced; taking the multiple conformers into account Our structural model supports the concept of "conformer selection"; which emphasize the, conformational flexibility of N-glycans in protein-glycan interactions.
• The Intertransmembrane Region of Kaposi's Sarcoma-Associated Herpesvirus Modulator of Immune Recognition 2 Contributes to B7-2 Downregulation

  Mizuho Kajikawa; Pai-Chi Li; Eiji Goto; Naoyuki Miyashita; Masami Aoki-Kawasumi; Mari Mito-Yoshida; Mika Ikegaya; Yuji Sugita; Satoshi Ishido

  JOURNAL OF VIROLOGY AMER SOC MICROBIOLOGY 86 (9) 5288 - 5296 0022-538X 2012/05 [Refereed]
   

  Kaposi's sarcoma-associated herpesvirus (KSHV), a human tumor virus, encodes two homologous membrane-associated E3 ubiquitin ligases, modulator of immune recognition 1 (MIR1) and MIR2, to evade host immunity. Both MIR1 and MIR2 downregulate the surface expression of major histocompatibility complex class I (MHC I) molecules through ubiquitin-mediated endocytosis followed by lysosomal degradation. Since MIR2 additionally downregulates a costimulatory molecule (B7-2) and an integrin ligand (intercellular adhesion molecule 1 [ICAM-1]), MIR2 is thought to be a more important molecule for immune evasion than MIR1; however, the molecular basis of the MIR2 substrate specificity remains unclear. To address this issue, we determined which regions of B7-2 and MIR2 are required for MIR2-mediated B7-2 downregulation. Experiments with chimeras made by swapping domains between human B7-2 and CD8 alpha, a non-MIR2 substrate, and between MIR1 and MIR2 demonstrated a significant contribution of the juxtamembrane (JM) region of B7-2 and the intertransmembrane (ITM) region of MIR2 to MIR2-mediated downregulation. Structure prediction and mutagenesis analyses indicate that Phe119 and Ser120 in the MIR2 ITM region and Asp244 in the B7-2 JM region contribute to the recognition of B7-2 by MIR2. This finding provides new insight into the molecular basis of substrate recognition by MIR family members.
• 1PT212 Effect of Bisecting GlcNAc and Core Fucosylation on Conformational Properties of Biantennary Complex-Type N-Glycans in Solution(The 50th Annual Meeting of the Biophysical Society of Japan)

  Nishima Wataru; Miyashita Naoyuki; Yamaguchi Yoshiki; Sugita Yuji; Suyong Re

  Seibutsu Butsuri The Biophysical Society of Japan General Incorporated Association 52 S104  2012
• 3E1110 Replica-exchange interface program (REIN)(Proteins:Structure,Oral Presentation)

  Miyashita Naoyuki; Re Suyong; Sugita Yuji

  Seibutsu Butsuri The Biophysical Society of Japan General Incorporated Association 52 S65  2012
• 3B1022 A computational Investigation into the MHC-I Recognition Mechanism of MIR2 from Kaposi's Sarcoma-Associated Herpesvirus(Proteins:Structure & Function III:Dynamics and Circadian Rhythm,Oral Presentation,The 50th Annual Meeting of the Biophysical Society of Japan)

  Li Pai-Chi; Miyashita Naoyuki; Ishido Satoshi; Sugita Yuji

  Seibutsu Butsuri The Biophysical Society of Japan General Incorporated Association 52 S58 - S59 2012
• Conformational flexibility of N-glycans in solution studied by REMD simulations

  Suyong Re; Wataru Nishima; Naoyuki Miyashita; Yuji Sugita

  Biophysical Reviews 4 (3) 179 - 187 1867-2450 2012 [Refereed]
   

  Protein-glycan recognition regulates a wide range of biological and pathogenic processes. Conformational diversity of glycans in solution is apparently incompatible with specific binding to their receptor proteins. One possibility is that among the different conformational states of a glycan, only one conformer is utilized for specific binding to a protein. However, the labile nature of glycans makes characterizing their conformational states a challenging issue. All-atom molecular dynamics (MD) simulations provide the atomic details of glycan structures in solution, but fairly extensive sampling is required for simulating the transitions between rotameric states. This difficulty limits application of conventional MD simulations to small fragments like di- and tri-saccharides. Replica-exchange molecular dynamics (REMD) simulation, with extensive sampling of structures in solution, provides a valuable way to identify a family of glycan conformers. This article reviews recent REMD simulations of glycans carried out by us or other research groups and provides new insights into the conformational equilibria of N-glycans and their alteration by chemical modification. We also emphasize the importance of statistical averaging over the multiple conformers of glycans for comparing simulation results with experimental observables. The results support the concept of "conformer selection" in protein-glycan recognition. © 2012 International Union for Pure and Applied Biophysics (IUPAB) and Springer.
• Structural Diversity and Changes in Conformational Equilibria of Biantennary Complex-Type N-Glycans in Water Revealed by Replica-Exchange Molecular Dynamics Simulation

  Suyong Re; Naoyuki Miyashita; Yoshiki Yamaguchi; Yuji Sugita

  BIOPHYSICAL JOURNAL CELL PRESS 101 (10) L44 - L46 0006-3495 2011/11 [Refereed]
   

  Structural diversity of N-glycans is essential for specific binding to their receptor proteins. To gain insights into structural and dynamic aspects in atomic detail not normally accessible by experiment, we here perform extensive molecular-dynamics simulations of N-glycans in solution using the replica-exchange method. The simulations show that five distinct conformers exist in solution for the N-glycans with and without bisecting GlcNAc. Importantly, the population sizes of three of the conformers are drastically reduced upon the introduction of bisecting GlcNAc. This is caused by a local hydrogen-bond rearrangement proximal to the bisecting GlcNAc. These simulations show that an N-glycan modification like the bisecting GlcNAc selects a certain "key" (or group of "keys") within the framework of the "bunch of keys" mechanism. Hence, the range of specific glycan-protein interactions and affinity changes need to be understood in terms of the structural diversity of glycans and the alteration of conformational equilibria by core modification.
• Functionality Mapping on Internal Surfaces of Multidrug Transporter AcrB Based on Molecular Theory of Solvation: Implications for Drug Efflux Pathway

  Takashi Imai; Naoyuki Miyashita; Yuji Sugita; Andriy Kovalenko; Fumio Hirata; Akinori Kideras

  JOURNAL OF PHYSICAL CHEMISTRY B AMER CHEMICAL SOC 115 (25) 8288 - 8295 1520-6106 2011/06 [Refereed]
   

  AcrB is a membrane protein and a multidrug efflux transporter. Although the recently solved X-ray crystal structures of AcrB provide a rough sketch of how drugs efflux, the pathway and mechanism have not been completely elucidated. In this study, a ligand-mapping method based on the 3D-RISM molecular theory of solvation, which we recently developed, is applied to AcrB in order to identify the drug efflux pathway. We use a fragment-based approach as a strategy to map chemical functionality on the internal surfaces. A few "multifunctional" ligand-binding sites, which recognize various types of functional groups, are detected inside the porter domain. Spatial links between the multifunctional sites indicate a probable multidrug efflux pathway. The frustrated environment of the protein cavity constructed of weak interactions between ligand and protein may be a mechanism for allowing smooth transportation through the protein. Guided diffusion appears to be the main mechanism for efflux.
• Winter School 2011 for the Integrated Simulation of Living Matter

  Y. Ishimine; H. Urakubo; Y. Sunaga; G. Masumoto; K. Misawa; N. Miyashita

  BioSupercomputing Newsletter 4 11 - 11 2011 [Invited]
  
• 3G1534 A multi-dimensional umbrella sampling approach for structure prediction of transmembrane helical dimer(3G Protein: Structure 4,The 49th Annual Meeting of the Biophysical Society of Japan)

  Li Pai-Chi; Miyashita Naoyuki; Ishido Satoshi; Sugita Yuji

  Seibutsu Butsuri The Biophysical Society of Japan General Incorporated Association 51 S132  2011
• 3D0936 Prediction of dynamical conformation of biantennary complex-type N-glycan in water by replica-exchange molecular dynamics simulations(3D Protein: Structure & Function 2,The 49th Annual Meeting of the Biophysical Society of Japan)

  Re Suyong; Miyashita Naoyuki; Yamaguchi Yoshiki; Sugita Yuji

  Seibutsu Butsuri The Biophysical Society of Japan General Incorporated Association 51 S117  2011
• Structure prediction of APP fragments using Replica-exchange molecular dynamics simulation

  MIYASHITA NAOYUKI; SUGITA YUJI

  情報処理学会研究報告(CD-ROM) 2010 (4) ROMBUNNO.HPC-127,4  2186-2583 2010/12 [Refereed][Invited]
  
• The autoimmune TCR-Ob 2F3 can bind to MBP85-99/HLA-DR2 having an unconventional mode as in TCR-Ob 1A12

  Zenichiro Kato; Joel N. H. Stern; Hironori K. Nakamura; Naoyuki Miyashita; Kazuo Kuwata; Naomi Kondo; Jack L. Strominger

  MOLECULAR IMMUNOLOGY PERGAMON-ELSEVIER SCIENCE LTD 48 (1-3) 314 - 320 0161-5890 2010/11 [Refereed]
   

  The generation of T cell receptor (TCR) sequence diversity can produce forbidden clones able to recognize self-antigens Here the structure of the complex between a myelin basic protein peptide (MBP85-99) human leukocyte antigen (HLA)-DR2 (DRB1*1501/DRA) and TCR-Ob 2F3 the dominant autoimmune clone obtained from a multiple sclerosis (MS) patient has been determined using structural docking simulation and dynamics in silico and compared to the structure of TCR-Ob 1A12 complexes with the same MHC/peptide determined by X-ray crystallography The two TCRs differ by three amino acids in the CDR3 alpha and beta loops As the result different hydrogen bonds are formed between the two CDR3 beta loops and the peptide in the complexes of the simulated structures with three hydrogen bonds seen in the TCR-Ob 2F3 complex and five in the TCR-Ob 1A12 complex The two TCRs each located near the N-terminal end of the HLA-DR2 binding groove and both had an orthogonal binding axis but they deviated by about 10 Simulation methods such as structural docking and molecular dynamics as used here provide an avenue to understand molecular binding mode efficiently and more rapidly than obtaining multiple crystal structures when a large structural database is already available (C) 2010 Elsevier Ltd All rights reserved
• Structure prediction of APP fragments using Replica-exchange molecular dynamics simulation

  Naoyuki Miyashita; Yuji Sugita

  IPSJ SIG Notes 一般社団法人情報処理学会 2010 (4) 1 - 6 1884-0930 2010/10 [Refereed][Invited]
   

  Aggregation/oligomalization of Amyloid β (Aβ) peptide is an essential event of the pathogenesis of Alzheimer Disease (AD). The Aβ peptide is a product of cleavage of Amyloid precursor protein (APP) by β- and γ- secretases. We have studied the mechanisms of Aβpeptide production by tertiary structure prediction of APP fragments in the membrane using Replica-exchange molecular dynamics simulations.
• 2P042 Molecular dynamics study of transmembrane segments of MIRs(The 48th Annual Meeting of the Biophysical Society of Japan)

  Li Pai-Chi; Miyashita Naoyuki; Ishido Satoshi; Sugita Yuji

  Seibutsu Butsuri The Biophysical Society of Japan General Incorporated Association 50 (2) S89  2010
• 3P044 The development of multi-dimensional replica-exchange molecular dynamics program (REIN)(Protein: Structure & Function,The 48th Annual Meeting of the Biophysical Society of Japan)

  Miyashita Naoyuki; Ikeguchi Mitsunori; Sugita Yuji

  Seibutsu Butsuri The Biophysical Society of Japan General Incorporated Association 50 (2) S152 - S153 2010
• REPLICA-EXCHANGE MOLECULAR DYNAMICS SIMULATIONS OF AMYLOID PRECURSOR PROTEIN DIMER IN MEMBRANE

  Naoyuki Miyashita; Yuji Sugita

  QUANTUM BIO-INFORMATICS III: FROM QUANTUM INFORMATION TO BIO-INFORMATICS WORLD SCIENTIFIC PUBL CO PTE LTD 26 361 - + 1793-5121 2010 

  Aggregation of amyloid beta peptide (An) in the brain is the primary element in the pathogenesis of Alzheimer's disease. A beta is derived from amyloid precursor protein (APP) in the membrane due to the cleavages by beta- and gamma-secretases. Here, we predict the transmembrane structures of the wild-type and mutant APP in the biological membrane by replica-exchange molecular dynamics simulations. The simulations illustrate large conformational differences between the wild type and mutant APP fragments in the membrane. Dimerization of the wild type occurs due to the C alpha-H center dot center dot center dot O hydrogen bonds at the Gly-XXX-Gly motifs between two APP fragments, whereas the mutant dimer is stabilized by the interactions between hydrophobic side chains. We also observe the downward shift of gamma-cleavage site in the mutant APP, which may cause the prohibition of A beta production.
• Structures of beta-Amyloid Peptide 1-40, 1-42, and 1-55-the 672-726 Fragment of APP-in a Membrane Environment with Implications for Interactions with gamma-Secretase

  Naoyuki Miyashita; John E. Straub; D. Thirumalai

  JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AMER CHEMICAL SOC 131 (49) 17843 - 17852 0002-7863 2009/12 [Refereed]
   

  Aggregation of Amyloid beta (A beta) peptide has been linked to the neurodegenerative Alzheimer's Disease and implicated in other amyloid diseases including cerebral amyloid angiopathy. A beta peptide is generated by cleavage of the amyloid precursor protein (APP) by transmembrane proteases. It is crucial to determine the structures of beta-amyloid peptides in a membrane to provide a molecular basis for the cleavage mechanism. We report the structures of amyloid beta peptide (A beta(1-40) and A beta(1-42)) as well as the 672-726 fragment of APP (referred to as A beta(1-55)) in a membrane environment determined by replica-exchange molecular dynamics simulation. A beta(1-40) is found to have two helical domains A (13-22) and B(30-35) and a type I beta-turn at 23-27. The peptide is localized at the interface between membrane and: solvent. Substantial fluctuations in domain A are observed. The dominant simulated tertiary structure of A beta(1-40) is observed to be similar to the simulated A beta(1-42) structure. However, there are differences observed in the overall conformational ensemble, as characterized by the two-dimensional free energy surfaces. The fragment of APP (A beta(1-55)) is observed to have a long transmembrane helix. The position of the transmembrane region and ensemble of membrane structures are elucidated. The conformational transition between the transmembrane A beta(1-55) structure, prior to cleavage, and the A beta(1-40) structure, following cleavage, is proposed.
• Prediction of Transmembrane Dimer Structure of Amyloid Precursor Protein using Replica-Exchange Molecular Dynamics Simulations

  Naoyuki Miyashita; Yuji Sugita

  BioSupercomputing Newsletter 1 10 - 10 2009/10 [Invited]
  
• Transmembrane Structures of Amyloid Precursor Protein Dimer Predicted by Replica-Exchange Molecular Dynamics Simulations

  Naoyuki Miyashita; John E. Straub; D. Thirumalai; Yuji Sugita

  JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AMER CHEMICAL SOC 131 (10) 3438 - + 0002-7863 2009/03 [Refereed]
   

  AB peptide is an essential protein in the pathogenesis of Alzheimer's disease and is derived from amyloid precursor protein (APP) in the membrane by beta- and gamma-secretase cleavage. An experimental study has shown that a pairwise replacement of Gly with Leu in APP enhances homodimerization but Leads to a drastic reduction of AB secretion. To resolve this apparent discrepancy, we predicted the wild-type (WT) and mutant APP dimer conformations by replica-exchange molecular dynamics simulations using the implicit membrane model IMM1. The simulations illustrate large conformational differences between the WT and mutant APP fragments in the membrane. Dimerization of the WT is due to two C(alpha)-H center dot center dot center dot O hydrogen bonds between two APP fragments, whereas dimerization of the mutant is due to hydrophobic interactions. In the mutant, each APP fragment is more tilted, and the gamma-cleavage site is shifted toward the center of the membrane. This position produces a mismatch between the active site of gamma-secretase and the gamma-cteavage site of APP that might prohibit AB production.
• 3P-031 Molecular dynamics simulation studies on the differences in the binding mechanism of LILRB1/HLA-G and LILRB2/HLA-G(Protein:Structure & Function,The 47th Annual Meeting of the Biophysical Society of Japan)

  Miyashita Naoyuki; Maenaka Katsumi; Sugita Yuji

  Seibutsu Butsuri The Biophysical Society of Japan General Incorporated Association 49 S156  2009
• 3P-090 The dimer conformation of amyloid β precursor protein fragment in membrane(The 46th Annual Meeting of the Biophysical Society of Japan)

  Miyashita Naoyuki; Straub John E.; Sugita Yuji

  Seibutsu Butsuri The Biophysical Society of Japan General Incorporated Association 48 S141  2008
• 3P018 The Structure of Amyloid β Peptide 1-40 in the membrane and the 672-726 fragment of of APP(Proteins-structure and structure-function relationship,Poster Presentations)

  Miyashita Naoyuki; Straub John E.; Devarajan Thirumalai

  Seibutsu Butsuri The Biophysical Society of Japan General Incorporated Association 47 S207  2007
• Structural changes in the cytoplasmic domain of phospholamban by phosphorylation at Ser16: A molecular dynamics study

  Yuji Sugita; Naoyuki Miyashita; Takao Yoda; Mitsunori Ikeguchi; Chikashi Toyoshima

  BIOCHEMISTRY AMER CHEMICAL SOC 45 (39) 11752 - 11761 0006-2960 2006/10 [Refereed]
   

  Phospholamban is a 52-residue integral membrane protein that regulates the activity of the sarcoplasmic reticulum calcium pump in cardiac muscle. Its inhibitory action is relieved when phospholamban is phosphorylated at Ser16 by cAMP-dependent protein kinase. To computationally explore all possible conformations of the phosphorylated form, and thereby to understand the structural effects of phosphorylation, replica-exchange molecular dynamics (REMD) was applied to the cytoplasmic domain that includes Ser16. The simulations showed that (i) without phosphorylation, the region from Lys3 to Ser16 takes all alpha-helical conformations; (ii) when phosphorylated, the alpha-helix is partially unwound in the C-terminal part ( from Ser10 to Ala15) resulting in less extended conformations; (iii) the phosphate at Ser16 forms salt bridges with Arg9, Arg13, and/or Arg14; and (iv) the salt bridges with Arg13 and Arg14 distort the alpha-helix and induce unwinding of the C-terminal part. We then applied conventional all-atom molecular dynamics simulations to the full-length phospholamban in the phospholipid bilayer. The results were consistent with those obtained with REMD simulations, suggesting that the transmembrane part of phospholamban and the lipid bilayer itself have only minor effects on the conformational changes in the cytoplasmic domain. The distortions caused by the salt bridges involving the phosphate at Ser16 readily explain the relief of the inhibitory effect of phospholamban by phosphorylation, as they will substantially reduce the population of all helical conformations, which are presumably required for the binding to the calcium pump. This will also be the mechanism for releasing the phosphorylated phospholamban from kinase.
• Structural role of countertransport revealed in Ca2+ pump crystal structure in the absence of Ca2+

  K Obara; N Miyashita; C Xu; L Toyoshima; Y Sugita; G Inesi; C Toyoshima

  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA NATL ACAD SCIENCES 102 (41) 14489 - 14496 0027-8424 2005/10 [Refereed]
   

  Ca2+-ATPase of sarcoplasmic reticulum is an ATR-powered Ca2+ pump but also a H+ pump in the opposite direction with no demonstrated functional role. Here, we report a 2.4-angstrom-resolution crystal structure of the Ca2+ -ATPase in the absence of Ca2+ stabilized by two inhibitors, dibutyidihydroxybenzene, which bridges two transmembrane helices, and thapsigargin, also bound in the membrane region. Now visualized are water and several phospholipid molecules, one of which occupies a cleft between two transmembrane helices. Atomic models of the Ca2+ binding sites with explicit hydrogens derived by continuum electrostatic calculations show how water and protons fill the space and compensate charge imbalance created by Ca2+-release. They suggest that H+ countertransport is a consequence of a requirement for maintaining structural integrity of the empty Ca2+-binding sites. For this reason, cation countertransport is probably mandatory for all P-type ATPases and possibly accompanies transport of water as well.
• Protonation of the acidic residues in the transmembrane cation-binding sites of the Ca2+ pump

  Y Sugita; N Miyashita; M Ikeguchi; A Kidera; C Toyoshima

  JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AMER CHEMICAL SOC 127 (17) 6150 - 6151 0002-7863 2005/05 [Refereed]
  
• 1P105 The function of the proton-counter transport in Ca^<2+>ATPase of sarcoplasmic reticulm

  Miyashita N.; Sugita Y.; Ikeguchi M.; Toyoshima C.

  Seibutsu Butsuri The Biophysical Society of Japan General Incorporated Association 44 S56  2004
• Electronic and lattice dynamics in the photoinduced ionic-to-neutral phase transition in a one-dimensional extended Peierls-Hubbard model

  N Miyashita; M Kuwabara; K Yonemitsu

  JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN PHYSICAL SOC JAPAN 72 (9) 2282 - 2290 0031-9015 2003/09 [Refereed]
   

  Real-time dynamics of charge density and lattice displacements is studied during photoinduced ionic-to-neutral phase transitions by using a one-dimensional extended Peierls-Hubbard model with alternating potentials for the one-dimensional mixed-stack charge-transfer complex, TTF-CA. The time-dependent Schrodinger equation and the classical equation of motion are solved for the electronic and lattice parts, respectively. We show how neutral domains grow in the ionic background. As the photoexcitation becomes intense, more neutral domains are created. Above threshold intensity, the neutral phase is finally achieved. After the photoexcitation, ionic domains with wrong polarization also appear. They quickly reduce the averaged staggered lattice displacement, compared with the averaged ionicity. As the degree of initial lattice disorder increases, more solitons appear between these ionic domains with different polarizations, which obstruct the growth of neutral domains and slow down the transition.
• Coherence recovery and photoinduced phase transitions in one-dimensional halogen-bridged binuclear platinum complexes

  K Yonemitsu; N Miyashita

  PHYSICAL REVIEW B AMERICAN PHYSICAL SOC 68 (7) 075113(9)  1098-0121 2003/08 [Refereed]
   

  A photoinduced transition from a charge-density-wave (CDW) phase to a charge-polarization (CP) phase has been recently found in a one-dimensional halogen-bridged binuclear platinum complex R-4[Pt-2(pop)(4)I]nH(2)O [pop=P2O5H22-, R=(C2H5)(2)NH2]. Its mechanism is theoretically studied by solving the time-dependent Hartree-Fock equation for a one-dimensional two-band three-quarter-filled Peierls-Hubbard model. Above a threshold in the photoexcitation intensity, a transition takes place from the CDW to CP phases. The threshold intensity depends on the relative stability of these phases, which can be explained qualitatively by their diabatic potentials. However, the transition from the CP to CDW phases is hardly realized for two reasons: (i) low-energy charge-transfer processes occur only within a binuclear unit in the CP phase; (ii) it is difficult for the CDW order to become long ranged owing to its weak coherence. The effective transfer integrals required for the coherence are evaluated.
• Photoinduced dynamics of ionicity near the neutral-ionic phase boundary in a one-dimensional extended Peierls-Hubbard model

  N Miyashita; M Kuwabara; K Yonemitsu

  SYNTHETIC METALS ELSEVIER SCIENCE SA 135 (1-3) 645 - 646 0379-6779 2003/04 [Refereed]
   

  Dynamics of the ionicity after photoexcitations in mixed-stack charge-transfer complexes is numerically studied by using a one-dimensional extended Peierls-Hubbard model with alternating potentials at half filling. The time-dependent Schrodinger equation and the Newton equation are solved for the electronic and lattice parts, respectively. Fourier analysis is performed for the ionicity. During the photoinduced phase transition, slow components are dominant and very broad reflecting complex motion of domain walls and lattice displacements. After the transition, fast and slow oscillations are clearly seen, which correspond to the electronic and lattice motion, respectively.
• Photoexcited states and photoinduced dynamics in electronic phases of MMX-chain systems

  K Yonemitsu; N Miyashita; M Kuwabara

  SYNTHETIC METALS ELSEVIER SCIENCE SA 135 (1-3) 521 - 522 0379-6779 2003/04 [Refereed]
   

  In the one-dimensional two-band three-quarter-filled Peierls-Hubbard model for halogen-bridged binuclear metal complexes R-4[Pt-2(pop)(4)I]nH(2)O with counter ion R and pop=P2O5H22-, a transition from the charge-density-wave phase to the charge-polarization phase is photoinduced, but the opposite process is not. Its origin is explained by considering differences in low-energy photoexcitations in the two phases and coherence of respective order parameters. The different dynamics is demonstrated by solving the time-dependent Schrodinger equation.
• Domain-wall dynamics after photoexcitations near neutral-ionic phase transitions

  N Miyashita; M Kuwabara; K Yonemitsu

  PHASE TRANSITIONS TAYLOR & FRANCIS LTD 75 (7-8) 887 - 893 0141-1594 2002/10 [Refereed]
   

  Real-time dynamics of domain walls between the neutral and ionic phases just after photoexcitations is studied by fully solving the time-dependent Schrodinger equation for a one-dimensional extended Peierls-Hubbard (PH) model, not by relying on the adiabatic approximation. The unrestricted Hartree-Fock (HF) approximation is used for electrons, and the lattice displacements are treated classically. Three characteristic time scales are observed: rapid oscillation of ionicity owing to the local charge transfer; slow oscillation of lattice displacements; and even slower and collective motion of domain walls. Steady growth of a metastable domain is achieved after complicated competition of micro domains. The relevance to recently measured, time-resolved photoreflectance spectra in TTF-CA is discussed.
• Variation mechanisms of ground-state and optical-excitation properties in quasi-one-dimensional two-band electron systems

  K Yonemitsu; M Kuwabara; N Miyashita

  MOLECULAR CRYSTALS AND LIQUID CRYSTALS TAYLOR & FRANCIS LTD 379 (1) 467 - 474 1058-725X 2002 [Refereed]
   

  We study i) the ground-state and optical-excitation properties of halogen-bridged binuclear metal complexes, which are known as MMX chain compounds, by the strong-coupling expansion for a one-dimensional two-orbital extended Peierls-Hubbard model, and ii) the dynamics of domain walls between the neutral and ionic phases in mixed-stack charge-transfer complexes, by solving the time-dependent Schrodinger equation for a one-dimensional extended Peierls-Hubbard model with alternating energy levels. We find in i) that competition between electron-electron and electron-lattice interactions and competition between short- and long-range interactions are both important for the electronic phase variation, and in ii) that charge and lattice dynamics immediately after photoexcitations is complex and not explained simply within the domino picture.
• Influence of short-range interference on ionization threshold law

  Naoyuki Miyashita; Shinichi Watanabe; Michio Matsuzawa; Joseph H. Macek

  Physical Review A - Atomic, Molecular, and Optical Physics 61 (1) 3  1094-1622 2000 [Refereed]
   

  Electron-impact ionization of the collinear [Formula Presented] model atom is investigated in order to examine a nonclassical behavior of the ionization cross sections. Slightly above the ionization threshold, ab initio calculations reveal a distinctive dip due to short-range dynamics. The dip is a strongly energy-dependent feature in the usually smooth and structureless ionization cross section and is foreign to treatments based on classical, as well as semiclassical mechanics. The [Formula Presented] model thus serves as a counterexample to the standard Wannier treatment of near-threshold ionization. The hyperspherical hidden-crossing theory is applied to identify the origin of the dip. © 1999 The American Physical Society.
• Quantum effects and the role of the potential ridge in ionization threshold law

  N. Miyashita; D. Kato; S. Watanabe; M. Matsuzawa; J. Macek

  21 st International Conference on the Physics of Electronic and Atomic Collisions（Sendai,Japan July22-27,1999）．Abstracts of Contributed Papers,eds. Y. Itikawa, K. Okuno, H. Tanaka, A. Yagishita and M. Matsuzawa 247  1999/07
• イオン化状態におけるポテンシアルの形状と量子効果

  宮下尚之; 加藤大治; 渡邉信一; 松澤通生

  日本物理学会54回年会（広島, 1999年3月28日-3月31日）講演概要集, 29p-ZC-7 1999/03
• Quantum diffraction and threshold law for the Temkin-Poet model of electron-hydrogen ionization

  Naoyuki Miyashita; Daiji Kato; Shinichi Watanabe

  Physical Review A - Atomic, Molecular, and Optical Physics 59 (6) 4385 - 4389 1094-1622 1999 [Refereed]
   

  Relying on an entirely ab initio quantum-mechanical scheme, we investigate the threshold behavior of a model electron-impact ionization problem in which the target hydrogen atom interacts with the incident electron only by monopole. The total ionization cross section for a singlet is shown to follow the threshold law of an exponential form as proposed by Macek and Ihra [Phys. Rev. A 55, 2024 (1997)], thus supporting the argument based on the local instability of the “ridge” motion despite the reported absence of classical ridge trajectories. Below the classical threshold, quantum diffraction allows the two electrons to have a large probability amplitude in the region inaccessible to the classical trajectories. The energy distribution for singlet in final continuum channels is shown to have a hitherto unexpected V-shaped structure at energies between 0 and 1 a.u. above the ionization threshold. The V structure becomes sharper toward the threshold while it approaches the quadratic form surmised by Bray [Phys. Rev. Lett. 78, 4721 (1997)] at higher energies. © 1999 The American Physical Society.

Conference Activities & Talks

• Deep Neural Networkを用いたレプリカ温度調整法の開発  [Not invited]

  中条貴裕; 斎藤聖奈; 松倉里紗; 宮下尚之

  日本物理学会2023年春季大会  2023/03  オンライン開催  日本物理学会
  
• 共有結合型ペプチド薬剤とGST二量体との相互作用機構  [Not invited]

  松倉里紗; 瀧真清; 宮下尚之; 渡辺信一; Jay Yang

  日本物理学会2023年春季大会  2023/03  オンライン開催  日本物理学会
  
• DNNベースのタンパク質モーフィング手法を用いたモノアミン酸化酵素のダイナミクス解析  [Not invited]

  清岡亮太; 大多和克紀; 松倉里紗; 宮下尚之

  日本物理学会2023年春季大会  2023/03  オンライン開催  日本物理学会
  
• HPCを用いたアルツハイマー病関連タンパク質γ切断酵素とコレステロールとの相互作用  [Not invited]

  南知香; 宮下尚之

  超異分野学会東京大会2023  2023/03  九段会館テラスコンファレンス＆バケット（東京都）  リバネス
  
• MOLECULAR DYNAMICS STUDY OF THE MECHANISM OF THE CLIENT UNFOLDED PROTEIN DELIVERY FROM HSP40 TO HSP70  [Not invited]

  Lisa Matsukura; Naoyuki Miyashita

  Biophysical Society Annual Meeting BPS2023  2023/02  San Diego (USA)  Biophysical Society of America
  
• γ切断酵素と APP の結合過程におけるコレステロールの役割  [Not invited]

  南知香; 松倉里紗; 宮下尚之

  第36回分子シミュレーション討論会  2022/12  オンライン開催  分子シミュレーション学会
  
• Deep Neural Network を用いた形からアミノ酸配列提案するプログラムの並列学習器モデルの考察  [Not invited]

  岩野和哉; 清岡亮太; 宮下尚之

  第36回分子シミュレーション討論会  2022/12  オンライン開催  分子シミュレーション学会
  
• Molecular dynamics study of the interaction between a GST dimer and a novel peptidic covalent aptamer  [Not invited]

  Lisa Matsukura; Naoyuki Miyashita; Masumi Taki; Shinichi Watanabe; Jay Yang

  CBI学会2022年大会  2022/10  タワーホール船堀（東京都）  CBI学会
  
• Simulation study of the interaction between lipids and the complex structure of γ-secretase and APP or Notch  [Not invited]

  Chika Minami; Lisa Matsukura; Naoyuki Miyashita

  CBI学会2022年大会  2022/10  タワーホール船堀（東京都）  CBI学会
  
• Deep Neural Networkを用いたタンパク質アミノ酸変異部位の提案プログラムの開発  [Not invited]

  岩野和哉; 宮下尚之

  近畿大学大学院サイエンスネットワーク2022・第10回院生サミット  2022/10  東大阪市  近畿大学
  
• Simulation study of the dissociation mechanism of the PPRP with RNA  [Not invited]

  Sumile Tanaka; Lisa Matsukura; Masaki Ottawa; Naoyuki Miyashita

  第60回日本生物物理学会  2022/09  函館アリーナ・函館市民会館（函館市）  日本生物物理学会
  
• Coarse-grained model Simulation study of the docking process of γ-secretase and APP/ Notch  [Not invited]

  Chika Minami; Lisa Matsukura; Naoyuki Miyashita

  第60回日本生物物理学会  2022/09  函館アリーナ・函館市民会館（函館市）  日本生物物理学会
  
• Application of the Protein Morphing Method and the Semi-automatic Simplified Path Exploration to the Membrane Protein Dimers Dynamics  [Not invited]

  Ryota Kiyooka; Masaki Ottawa; Lisa Matsukura; Naoyuki Miyashita

  第60回日本生物物理学会  2022/09  函館アリーナ（北海道）  日本生物物理学会
  
• HSP40 binding affects the stability of HSP70  [Not invited]

  Lisa Matsukura; Naoyuki Miyashita

  第60回日本生物物理学会  2022/09  函館アリーナ（北海道）  日本生物物理学会
  
• アミロイド前駆体タンパク質と Notch 受容体の膜貫通部位とγ-切断酵素との相互作用とコレステロールとの関わり  [Not invited]

  南 知香; 松倉里紗; 宮下尚之

  日本物理学会2022年秋季大会  2022/09  東工大（東京）  日本物理学会
  
• ペプチド型共有結合薬剤とGSTタンパク質との結合構造に関する分子動力学シミュレーション  [Not invited]

  松倉里紗; 瀧真清; 宮下尚之; 渡辺信一

  日本物理学会2022年秋季大会  2022/09  オンライン  日本物理学会
  
• Deep Neural Networkを用いたタンパク質の構造データからアミノ酸配列を提案するプログラムの開発  [Not invited]

  岩野和哉; 清岡亮太; 宮下尚之

  日本物理学会2022年秋季大会  2022/09  東工大（東京）  日本物理学会
  
• タンパク質構造変化の反応経路の自動探索機能を導入した構造変化モーフィングプログラムの開発  [Not invited]

  清岡亮太; 松倉里紗; 大多和克紀; 福岡綺羅; 宮下尚之

  日本物理学会第77回年次大会  2022/03  オンライン  日本物理学会
  
• 分子動力学シミュレーションを用いたタウタンパク質ターゲットPET薬剤THK5351とモノアミン酸化酵素Bの相互作用の研究  [Not invited]

  大多和克紀; 中条貴裕; 松倉里紗; 宮下尚之; 原田龍一; 木村裕一; 古本祥三

  日本物理学会第77回年次大会  2022/03  オンライン  日本物理学会
  
• HSP70のシャペロンサイクルにおける構造変化とコシャペロンとの相互作用の動力学  [Not invited]

  松倉里紗; 宮下尚之

  日本物理学会第77回年次大会  2022/03  オンライン  日本物理学会
  
• rPPRPとRNAの配列にミスマッチがある場合の乖離メカニズム  [Not invited]

  田中寿美礼; 松倉里紗; 大多和克紀; 宮下尚之

  日本物理学会第77回年次大会  2022/03  オンライン  日本物理学会
  
• Interaction between Amyloid precursor protein and the transmembrane region of beta-secretase and the dynamics  [Not invited]

  Naoyuki Miyashita; Kaori Yanagino; Lisa Matsukura; Masaki Ottawa

  Pacifichem 2021,  2021/12  USA(Hawaii) + Online  Pacifichem
  
• Simulation study of the dynamics of the ligand entrance gate in Monoamine Oxidase B (MAO-B) and PET tracers  [Not invited]

  Masaki Ottawa; Lisa Matsukura; Naoyuki Miyashita; Ryuichi Harada; Yuichi Kimura; Shozo Furumoto

  Pacifichem 2021  2021/12  Honolulu (online)  Pacifichem 2021
  
• A simulation study of the HSP90 chaperone cycle and new HSP90 inhibitor  [Not invited]

  Lisa Matsukura; Naoyuki Miyashita

  Pacifichem 2021  2021/12  Honolulu (online)  Pacifichem 2021
  
• 粗視化モデル分子動力学シミュレーションを用いたNotchとγ切断酵素の相互作用とその結合機構  [Not invited]

  南知香; 宮下尚之

  第44回分子生物学会  2021/12  パシフィコ横浜  分子生物学会
  
• 分子動力学を用いた不均衡データ補間とディープラーニングを用いたタンパク質構造変化モーフィング  [Not invited]

  清岡亮太; 松倉里紗; 大多和克紀; 福岡綺羅; 宮下尚之

  第35回分子シミュレーション討論会  2021/11  オンライン  分子シミュレーション学会
  
• ラフト環境下におけるγ切断酵素とそれによって切断される膜タンパク質の膜貫通部位と脂質分子の相互作用  [Not invited]

  南知香; 宮下尚之

  第35回分子シミュレーション討論会  2021/11  オンライン  分子シミュレーション学会
  
• Development of the Morphing Program for Protein Structural Changes on 3D Reaction Coordinates Using DNN and MD Simulations  [Not invited]

  Ryota Kiyooka; Lisa Matsukura; Masaki Ottawa; Kira Fukuoka; Naoyuki Miyashita

  第59回日本生物物理学会  2021/11  オンライン  日本生物物理学会
  
• HSP70とHSP40の複合体のダイナミクスとHSP70のLidドメインの役割に関するシミュレーション  [Not invited]

  Lisa Matsukura; Naoyuki Miyashita

  第59回日本生物物理学会  2021/11  オンライン  日本生物物理学会
  
• Interaction Between Cholesterol and Substrate Binding Sites of 𝛾-secretase  [Not invited]

  Chika Minami; Naoyuki Miyashita

  59th Conference of Biophysical Society of Japan  2021/11  オンライン  日本生物物理学会
  
• タウタンパク線維部分モデルの分子動力学シミュレーションとPET薬剤結合部位  [Not invited]

  Masaki Ottawa; Lisa Matsukura; Naoyuki Miyashita; Ryuichi Harada; Yuichi Kimura; Shozo Furumoto

  日本物理学会2021年秋季大会  2021/09  オンライン  日本物理学会
  
• 分子動力学シミュレーションとディープニューラルネットワークを用いたタンパク質構造変化モーフィングプログラムの開発と応用  [Not invited]

  Ryota Kiyooka; Lisa Matsukura; Masaki Ottawa; Naoyuki Miyashita

  日本物理学会2021年秋季大会  2021/09  オンライン  日本物理学会
  
• 分子動力学シミュレーションを用いたHSP70のopen-close状態の違い  [Not invited]

  Lisa Matsukura; Naoyuki Miyashita

  日本物理学会2021年秋季大会  2021/09  オンライン  日本物理学会
  
• 分子動力学シミュレーションを用いたアルツハイマー病関連タンパク質APP，シグナル伝達タンパク質Notch，γ切断酵素の脂質分子との相互作用機構  [Not invited]

  Chika Minami; Lisa Matsukura; Masaki Ottawa; Naoyuki Miyashita

  日本物理学年秋季大会  2021/09  オンライン  日本物理学会
  
• ATP結合型と非結合型HSP70のダイナミクスの違い  [Not invited]

  Lisa Matsukura; Naoyuki Miyashita

  第15回分子科学討論会  2021/09  オンライン  日本分子科学会
  
• Interaction between PET tracer and the specific residues around the gate of the open form of Monoamine Oxidase B (MAO-B)  [Not invited]

  Masaki Ottawa; Lisa Matsukura; Naoyuki Miyashita; Ryuichi Harada; Yuichi Kimura; Shozo Furumoto

  CCP2021  2021/08  Coventry, England (online)  Computational physics
  
• Simulation study of the function of domain swapping in the HSP90 chaperone cycle  [Not invited]

  Lisa Matsukura; Naoyuki Miyashita

  CCP2021 (XXXII IUPAP Conference on Computational Physics)  2021/08  Coventry, England (Online)  Computational physics
  
• The stability of HSP90NTD and ch-chaperone p23 by the domain swapping in HSP90 dimer  [Not invited]

  Lisa Matsukura; Naoyuki Miyashita

  第21回日本蛋白質科学会年会  2021/06  オンライン
• The Prediction of the Structure Changes of ADK along the Reaction Coordinate using Deep Neural Network and Molecular Dynamics Simulations.  [Not invited]

  Ryota Kiyooka; Lisa Matsukura; Masaki Ottawa; Naoyuki Miyashita

  第21回日本蛋白質科学会  2021/06  オンライン
• The difference between the interaction of lipids and Notch receptor and that of lipids and Amyloid precursor protein.  [Not invited]

  Chika Minami; Kaori Yanagino; Lisa Matsukura; Masaki Ottawa; Naoyuki Miyashita

  第21回日本蛋白質科学会  2021/06  オンライン
• 分子動力学シミュレーションとニューラルネットワークを用いたタンパク質構造変化モーフィング法  [Not invited]

  Ryota Kiyooka; Lisa Matsukura; Masaki Ottawa; Naoyuki Miyashita

  日本コンピュータ化学会  2021/06  オンライン
• HSP90とコシャペロンの分子動力学シミュレーション  [Not invited]

  松倉里紗; 宮下尚之

  日本コンピュータ化学会  2021/06  オンライン
• モノアミン酸化酵素B（MAO-B）の薬剤結合部位の動力学とそのPETトレーサーSMBT-1との相互作用  [Not invited]

  大多和克紀; 松倉里紗; 宮下尚之; 原田龍一; 木村裕一; 古本祥三

  第23回理論化学討論会  2021/05  オンライン
• HSP90の分子動力学シミュレーションとドメインスワッピングの機能  [Not invited]

  松倉里紗; 宮下尚之

  第23回理論化学討論会  2021/05  オンライン
• 粗視化モデルシミュレーションを用いた脂質分子とγ切断酵素との相互作用研究  [Not invited]

  Chika Minami; Kaori Yanagino; Naoyuki Miyashita

  第23回理論化学討論会  2021/05  オンライン
• The effect of the interaction between HSP90 and co-chaperone by novel HSP90 inhibitor  [Not invited]

  Lisa Matsukura; Naoyuki Miyashita

  日本物理学会第76回年次大会(2021年)  2021/03  オンライン
• 生体膜中におけるAPPとα-/β-切断酵素との相互作用機構  [Not invited]

  柳野賀緒梨; 大多和克紀; 松倉里紗; 宮下尚之

  日本物理学会第76回年次大会(2021年)  2021/03  オンライン
• モノアミン酸化酵素B(MAO-B)の薬剤結合部位のダイナミクスとPETトレーサーの結合  [Not invited]

  大多和克紀; 松倉里紗; 宮下尚之; 原田龍一; 木村裕一; 古本祥三

  日本物理学会第76回年次大会(2021年)  2021/03  オンライン
• Notch受容体の膜貫通部位と脂質分子との相互作用  [Not invited]

  Chika Minami; Kaori Yanagino; Naoyuki Miyashita

  日本物理学会第76回年次大会(2021年)  2021/03  オンライン
• 分子シミュレーションで見るアルツハイマー病初期過程で働く膜タンパク質と脂質分子との相互作用  [Invited]

  宮下尚之

  蛋白質研究所セミナー『生体膜上の生物化学 ー解析法の進展から細胞内オルガネラのバイオロジーまでー』  2021/03  オンライン
• DETAIL DYNAMICS AFTER ATP BINDING IN HSP90 CHAPERONE CYCLE AND THE EFFECT OF NOVEL PEPTIDE DRUG CANDIDATE USING MOLECULAR DYNAMICS SIMULATIONS  [Not invited]

  Lisa Matsukura; Naoyuki Miyashita

  65th Biophysical Society Annual Meeting BPS2021  2021/02  オンライン
• STRUCTURE PREDICTION OF THE TRANSMEMBRANE REGION OF ALPHA- AND BETA- SECRETASES USING REPLICA-EXCHANGE MOLECULAR DYNAMICS SIMULATIONS, AND THE INTERACTION BETWEEN AMYLOID PRECURSOR PROTEIN AND THEM  [Not invited]

  Kaori Yanagino; Naoyuki Miyashita

  65th Biophysical Society Annual Meeting BPS2021  2021/02  オンライン開催
• α切断酵素とβ切断酵素の膜貫通部位の構造予測とそのダイナミクス  [Not invited]

  柳野賀緒梨; 宮下尚之

  第34回分子シミュレーション討論会  2020/12  オンライン開催
• 分子シミュレーションを用いたHSP90機能阻害薬の作用機構の解明  [Not invited]

  松倉里紗; 宮下尚之; 瀧真清

  第34回分子シミュレーション討論会  2020/12  オンライン開催
• MAO-Bのリガンド結合部位の同力学とPET薬剤の結合自由エネルギー  [Not invited]

  大多和克紀; 松倉理紗; 宮下尚之; 原田龍一; 木村裕一; 古本祥三

  第34回分子シミュレーション討論会  2020/12  オンライン開催
• α切断酵素の膜貫通部位の構造予測とAPPの膜貫通部位との相互作用  [Not invited]

  柳野賀緒梨; 宮下尚之

  第43回日本分子生物学会年会  2020/12  オンライン開催
• HSP90-NTD二量体におけるドメインスワッピングの機能  [Not invited]

  松倉里紗; 瀧真清; 渡辺信一; 宮下尚之

  第43回日本分子生物学会年会  2020/12  オンライン開催
• MAO-Bとタウ蛋白質の薬剤結合  [Not invited]

  大多和克紀; 松倉里紗; 宮下尚之; 原田龍一; 木村裕一; 古本祥三

  第43回日本分子生物学会年会  2020/12  オンライン開催
• New Peptide Drug and the Molecular Dynamics Simulations of Target Protein and the New Drug  [Invited]

  Lisa Matsukura; Naoyuki Miyashita; Masumi Taki; Shinichi Watanabe

  第58回日本生物物理学会年会,オンライン開催  2020/09
• Interaction Between beta-Secretase and APP in The Biological Membrane, and The Structure Prediction of The TM domain of alpha-Secretase.  [Not invited]

  Kaori Yanagino; Naoyuki Miyashita

  第58回日本生物物理学会年会, オンライン開催  2020/09
• The dynamics of dopamine-regulated protein MAO-B in the mitochondrial membrane  [Not invited]

  MasakiOttawa; LisaMatsukura; NaoyukiMiyashita; RyuichiHarada, YuichiKimura; SyozoFurumoto

  第58回日本生物物理学会年会, オンライン開催  2020/09
• HSP90二量体のシミュレーションと新規薬剤との相互作用１  [Not invited]

  松倉里紗; 宮下尚之; 瀧真清; 渡辺信一

  日本物理学会2020年秋季大会，オンライン開催  2020/09
• β切断酵素とAPPの膜貫通部位の相互作用インターフェース  [Not invited]

  柳野賀緒梨; 宮下尚之

  日本物理学会2020年秋季大会，オンライン開催  2020/09
• 生体膜環境下におけるMAO-Bの長時間分子動力学シミュレーションと薬剤結合  [Not invited]

  大多和克紀; 松倉里紗; 柳野賀緒梨; 宮下尚之; 原田龍一; 木村裕一; 古本祥三

  日本物理学会2020年秋季大会，オンライン開催  2020/09
• Molecular Dynamics Simulation of HSP90 Dimer and Docking Simulation of the Peptide Drug  [Not invited]

  Lisa Matsukura; Naoyuki Miyashita; Masumi Taki; Shinichi Watanabe

  タンパク質科学会, SORA札幌コンベンションセンター（北海道）  2020/07
• Structure Prediction of the transmembrane domain of alpha- and beta-secretases and the structural differences  [Not invited]

  Kaori Yanagino; Naoyuki Miyashita

  第20回日本蛋白質科学会年会，SORA札幌コンベンションセンター（北海道）  2020/07
• コンピュータシミュレーションを用いたアルツハイマー病の初期分子機構にかかわるβ切断酵素のダイナミクス

  柳野賀緒梨; 宮下尚之

  第9回超異分野本大会，WEB開催  2020/04
• 粗視化モデルシミュレーションを用いたチロシンキナーゼの膜貫通部位のラフト中の二量体形成  [Not invited]

  井本誓龍; 南知香; 柳野賀緒梨; 松倉里紗; 宮下尚之

  第75回日本物理学会（２０２０年）年次大会, 名古屋大学（名古屋）WEB開催  2020/03
• ドッキングシミュレーションを用いたHSP90と中分子薬の結合機構  [Not invited]

  松倉里紗; 望月和人; 宮下尚之; 瀧真清; 渡辺信一

  第75回日本物理学会（２０２０年）年次大会, 名古屋大学（名古屋）WEB開催  2020/03
• μ秒の分子動力学シミュレーションを用いたCRISPR Cas3のDNAとの相互作用機構解析  [Not invited]

  山口知洋; 宮下尚之

  第75回日本物理学会（２０２０年）年次大会, 名古屋大学（名古屋）WEB開催  2020/03
• アルツハイマー病初期過程におけるβ切断酵素とAPPの相互作用機構  [Not invited]

  柳野賀緒梨; 南知香; 宮下尚之

  第75回日本物理学会（２０２０年）年次大会, 名古屋大学（名古屋）WEB開催  2020/03
• 学習データの自動選択法を取り入れたDeep Learningによる水溶液中タンパク質のホモロジーモデリング手法の開発  [Not invited]

  古江 祐也; 松倉里紗; 大多和克紀; 宮下尚之

  第75回日本物理学会（２０２０年）年次大会, 名古屋大学（名古屋）WEB開催  2020/03
• MAO-Bの長時間分子動力学シミュレーションによる薬剤結合部位の動力学解析  [Not invited]

  大多和克紀; 松倉里紗; 田中良奈; 柳野賀緒梨; 宮下尚之; 木村裕一; 古本祥三

  第75回日本物理学会（２０２０年）年次大会, 名古屋大学（名古屋）WEB開催  2020/03
• Deep Learningを用いたタンパク質欠損部位構造モデリングソフトウエアの開発  [Not invited]

  高見拓磨; 古江祐也; 土井直哉; 宮下尚之

  第75回日本物理学会（２０２０年）年次大会, 名古屋大学（名古屋）WEB開催  2020/03
• BINDING MECHANISM OF ANTI-CANCER TARGET HSP90 AND PEPTIDE DRUG  [Not invited]

  Lisa Matsukura; Naoyuki Miyashita

  64th Annual Meeting of the Biophysical Society  2020/02  San Diego Convention Center San Diego, California, USA  Biophysical society
  
• Deep learning を用いたタンパク質欠損部位モデリングの試み  [Not invited]

  高見 拓磨; 古江祐也; 山口知洋; 宮下尚之

  第33回分子シミュレーション討論会  2019/12  名古屋市公会堂（名古屋）
• CRISPR Cas3のDNAとの相互作用機構  [Not invited]

  山口知洋; 宮下尚之

  第33回分子シミュレーション討論会  2019/12  名古屋市公会堂（名古屋）
• アルツハイマー病初期分子機構に関係するβ切断酵素の膜貫通部位の構造予測トラフトとの相互作用  [Not invited]

  柳野賀緒梨; 古江祐也; 宮下尚之

  第33回分子シミュレーション討論会  2019/12  名古屋市公会堂（名古屋）
• 力学的安定性の高いモデル構造を生成するためのDeep Learning を用いたホモロジーモデリング  [Not invited]

  古江祐也; 松倉 里紗; 宮下尚之

  第33回分子シミュレーション討論会  2019/12  名古屋市公会堂（名古屋）
• 新規ペプチド薬のHSP90との結合機構・機能阻害メカニズム  [Not invited]

  松倉 里紗; 望月和人; 宮下尚之; 瀧真清; 渡辺信一

  第33回分子シミュレーション討論会  2019/12  名古屋市公会堂（名古屋）
• HSP90の分子動力学シミュレーションと新規中分子薬による機能阻害機構  [Not invited]

  Lisa Matsukura; Kazuto Mochizuki; Naoyuki Miyashita; Masumi Taki; Shinichi Watanabe

  第42回日本分子生物学会年会  2019/12  福岡国際会議場・マリンメッセ福岡(福岡)
• α切断酵素とβ切断酵素の膜貫通部位の構造予測とラフト環境との相互作用  [Not invited]

  Kaori Yanagino; Naoyuki Miyashita

  第42回日本分子生物学会年会  2019/12  福岡国際会議場・マリンメッセ福岡(福岡)
• MOLECULAR DYNAMICS SIMULATION STUDY FOR THE DIFFERENCES BETWEEN THE DYNAMICS OF CRISPR CAS3 WITH AND WITHOUT SHORT SINGLE-STRAND DNA  [Not invited]

  Tomohiro Yamaguchi; Naoyuki Miyashita

  Frontiers in Genome Engineering 2019,  2019/11  Kobe
• Molecular Dynamics Simulations of CRISPR Type I-E System and the DNA binding Mechanisms  [Not invited]

  Naoyuki Miyashita; Tomohiro Yamaguchi; Lisa Matsukura; Masaya Furue

  The 5th International Conference on Molecular Simulation,  2019/11  Lotte Hotel Jeju (Korea)
• The Stability of a Stapled Peptide Drug and the Inhibition Mechanism of HSP90 Function using Long-time Molecular Dynamics Simulations  [Not invited]

  Lisa Matsukura; Kazuto Mochizuki; Naoyuki Miyashita; Masumi Taki; Shinichi Watanabe

  The 5th International Conference on Molecular Simulation  2019/11  Lotte Hotel Jeju (Korea),
• Homology Modeling of the Protein Structure in the Solution using Deep Auto Encoder and Trajectories of the Long-time Molecular Dynamics Simulation of Template Proteins

  Masaya Furue; Lisa Matsukura; Mitsutaka Nemoto; Naoyuki Miyashita

  CBI学会2019年大会  2019/10  タワーホール船堀(東京)
• The inhibition mechanism of HSP90 function by a medium molecular drug  [Not invited]

  Lisa Matsukura; Kazuto Mochizuki; Naoyuki Miyashita; Masumi Taki; Shinichi Watanabe

  CBI学会2019年大会  2019/10  タワーホール船堀(東京)
• Molecular dynamics simulation of the biomolecules that related to the future biomedicine  [Not invited]

  Lisa Matsukura; Naoyuki Miyashita

  11th symposium on Discovery, Fusion, Creation of New Knowledge by Multidisciplinary Computational Sciences, CCS International Symposium 2019, International Congress Center EPOCHAL TSUKUBA (Tsukuba),  2019/10
• Molecular dynamics simulations of CRISPR Cas3 and Cse1 complex  [Not invited]

  ◯Tomohiro Yamaguchi; Yui Taketomo; Naoyuki Miyashita

  第57回日本生物物理学会年会  2019/09  シーガイア・宮崎市  日本生物物理学会
  
• Development of Deep-Autoencoder based Homology Modeling software  [Not invited]

  ◯Masaya Furue; Mitsutaka Nemoto; Lisa Matsukura; Naoyuki Miyashita

  第57回日本生物物理学会年会  2019/09  シーガイア・宮崎市  日本生物物理学会
  
• Influence on the structure and dynamics of Riboswitch “SPINACH” and potassium ions by DFHBI  [Not invited]

  ◯Lisa Matsukura; Nobutaka Onishi; Masaya Furue; Naoyuki Miyashita; Takuma Shiraki; Yasushige Yonezawa

  第57回日本生物物理学会年会  2019/09  シーガイア・宮崎市  日本生物物理学会
  
• Interaction between amyloid precursor protein and beta-secretase in the bio-membrane  [Not invited]

  ◯Kaori Yanagino; Naoyuki Miyashita

  第57回日本生物物理学会年会  2019/09  シーガイア・宮崎市  日本生物物理学会
  
• mDeepHoMe : Deep Learningを用いた水和環境下のターゲットタンパク質のホモロジーモデリング  [Not invited]

  古江 祐也; 根本 充貴; 宮下 尚之

  日本物理学会2019年秋季物理学会  2019/09
• mDeepHoMe : Deep Learningを用いた水和環境下のターゲットタンパク質のホモロジーモデリング  [Not invited]

  古江 祐也; 根本 充貴; 宮下 尚之

  日本物理学会2019年秋季物理学会  2019/09  岐阜大学（岐阜市）  日本物理学会
  
• CRISPR Cas3の分子ダイナミクス  [Not invited]

  山口知洋; 竹友唯; 宮下尚之

  日本物理学会2019年秋季物理学会  2019/09  岐阜大学（岐阜市）  日本物理学会
  
• アルツハイマー病関連タンパク質であるβ切断酵素の膜貫通部位とラフトとの相互作用  [Not invited]

  柳野 賀緒梨; 宮下 尚之

  日本物理学会2019年秋季物理学会  2019/09  岐阜大学（岐阜市）  日本物理学会
  
• Molecular Dynamics Simulation of CRISPR Cas3  [Not invited]

  ○Tomohiro Yamaguchi; Yui Takatomo; Naoyuki Miyashita

  第19回 日本蛋白質科学会年会  2019/06  神戸国際会議場（神戸）  日本タンパク質科学会
  
• Structure Prediction of Transmembrane domain of beta-secretase  [Not invited]

  ◯Kaori Yanagino; Naoyuki Miyashita

  第19回 日本蛋白質科学会年会, 神戸国際会議場（神戸）  2019/06  神戸国際会議場（神戸）  日本タンパク質科学会
  
• Mechanism of the interaction between Hsp90 and the medium molecule drug, and the docking simulation  [Not invited]

  ○Lisa Matsukura; Kazuto Mochizuki; Masaya Furue; Masumi Taki; Naoyuki Miyashita

  第19回 日本蛋白質科学会年会  2019/06
• Development of Homology modeling program using Deep Learning  [Not invited]

  ○Masaya Furue; Lisa Matsukura; Mitsutaka Nemoto; Naoyuki Miyashita

  第19回 日本蛋白質科学会年会  2019/06  神戸国際会議場（神戸）  日本タンパク質科学会
  
• Dynamics of CRISPR Cas System  [Not invited]

  ○Naoyuki Miyashita; Yui Taketomo; Tomohiro Yamaguchi; Lisa Matsukura; Ryo Ohashi

  第19回 日本蛋白質科学会年会  2019/06  神戸国際会議場（神戸）  日本タンパク質科学会
  
• 中分子薬剤とHsp90との相互作用  [Not invited]

  松倉里紗; 望月和人; 古江祐也; 宮下尚之; 瀧真清; 渡辺信一

  第22回理論化学討論会  2019/05  北海道大学(学術交流会館)（札幌市）  理論化学会
  
• アルツハイマー病の初期分子機構と分子シミュレーション  [Not invited]

  宮下尚之

  東京薬科大学生命科学部理論系合同セミナー  2019/05  東京薬科大学 (東京都)  東京薬科大学
  
• 長時間分子動力学シミュレーションによるCRISPR Type I-EのcrRNA安定化機構とそのダイナミクス  [Not invited]

  竹友唯; 山口知洋; 古江祐也; 宮下尚之

  日本物理学会第７４回年次大会  2019/03  九州大学（福岡市）  日本物理学会
  
• β切断酵素の膜貫通部位の構造予測と生体膜中でのダイナミクス  [Not invited]

  柳野賀緒梨; 高橋良太; 古江祐也; 宮下尚之

  日本物理学会第７４回年次大会  2019/03  九州大学（福岡市）  日本物理学会
  
• 分子動力学に基づいた深層学習による新規ホモロジーモデリングプログラムの開発  [Not invited]

  古江祐也; 根本充貴; 宮下尚之

  日本物理学会第７４回年次大会  2019/03  九州大学（福岡市）  日本物理学会
  
• 長時間MDシミュレーションを用いたHsp90と中分子薬の結合機構の提案  [Not invited]

  松倉里紗; 望月和人; 古江祐也; 宮下尚之; 瀧真清; 渡辺信一

  日本物理学会第７４回年次大会  2019/03  九州大学（福岡市）  日本物理学会
  
• 分子シミュレーションとそのビッグデータ解析による新規中分子薬結合メカニズムの検討  [Not invited]

  松倉里紗; 望月和人; 古江祐也; 宮下尚之; 瀧真清; 渡辺信一

  平成31年度 和歌山大学システム工学部・近畿大学生物理工学部学生成果発表会  2019/03  ルミエール華月殿（和歌山市）  和歌山産業振興財団・和歌山情報サービス産業協会WAKASA
  
• 近畿大学生物理工学部電算機センターHPCとアルツハイマー病初期過程の分子機構  [Invited]

  宮下尚之

  第４回 近畿大学 認知症 Core 研究(DoIK)シンポジウムー認知症克服に向けた工学的アプローチ  2019/03  近畿大学（東大阪）  近畿大学
  
• Molecular Dynamics Simulation of Module-Type CRISPR System  [Not invited]

  Naoyuki Miyashita

  CCS International Symposium 2018 10th symposium on Discovery, Fusion, Creation of New Knowledge by Multidisciplinary Computational Sciences  2018/10  Tsukuba  Tsukuba University
  
• Development of Template-Based Protein Structure Modeling Method Using Deep-Autoencoder with a Denoising Algorithm  [Not invited]

  Masaya Furue; Mitsutaka Nemoto; Naoyuki Miyashita

  CBI学会2018年大会  2018/10  タワーホール船堀（東京都）  CBI学会
  
• Microsecond Molecular Dynamics Simulations of Medium Molecule Drugs and the docking with a target protein  [Not invited]

  Lisa Matsukura; Kazuto Mochizuki; Masumi Taki; Shinichi Watanabe; Naoyuki Miyashita

  CBI学会2018年大会  2018/10  タワーホール船堀（東京都）  CBI学会
  
• アルツハイマー病の初期機構に関わる生体分子の形と動きを分子シミュレーションで見る  [Invited]

  宮下尚之

  CBI学会2018年大会  2018/10  タワーホール船堀（東京都）  CBI学会
  
• The dynamics of CRISPR-CMR before/after the cleavage of targeted RNA  [Not invited]

  ○Tomohiro Yamaguchi; Ryo Ohashi; Naoyuki Miyashita

  日本生物物理学会第56回年会  2018/09  岡山大学(岡山市)  日本生物物理学会
  
• Dynamics of the cleavage of DNA/RNA in module type CRISPR/CAS system by using molecular dynamics  [Not invited]

  Naoyuki Miyashita; Ryo Ohashi; Reiwat Takeuchi; Yui Taketomo

  日本生物物理学会第56回年会  2018/09  岡山大学(岡山市)  日本生物物理学会
  
• Dynamics of peptide aptamer which targeting Hsp90 and the development of supporting program for modification of force field parameters  [Not invited]

  ○Lisa Matsukura; Kazuto Mochizuki; Masumi Taki; Naoyuki Miyashita

  日本生物物理学会第56回年会  2018/09  岡山大学(岡山市)  日本生物物理学会
  
• Development of Template-based Protein Structure Modeling Software using Molecular Dynamics Simulations of Template proteins.  [Not invited]

  Masaya Furue; Mitsutaka Nemoto; Naoyuki Miyashita

  日本生物物理学会第56回年会  2018/09  岡山大学(岡山市)  日本生物物理学会
  
• 深層学習による複数テンプレートを用いたタンパク質モデリング  [Not invited]

  古江 祐也; 根本充貴; 宮下尚之

  日本物理学会2018年秋季大会  2018/09  同志社大学（京田辺市）  日本物理学会
  
• ゲノム編集タンパク質の核酸切断動力学と分子内情報伝達  [Invited]

  宮下尚之

  蛋白研セミナー「生体分子内情報伝達の新展開」  2018/09  大阪大学(大阪府吹田市)  大阪大学蛋白質研究所
  
• Dynamics of the gate of DFHBI and Ions in riboswitch SPINACH  [Not invited]

  Naoyuki Miyashita; Nobutaka Onishi; Masaya Furue; Takuma Shiraki; Yasushige Yonezawa

  The 256th ACS National Meeting (アメリカ化学会)  2018/08  ボストン（アメリカ国）  アメリカ化学会
  
• CRISPR CMRのDNA切断動力学  [Not invited]

  宮下尚之; 大橋燎; 山口和洋

  第１８回日本蛋白質科学会年会  2018/06  新潟市  日本蛋白質科学会
  
• スーパーコンピュータは顕微鏡 --アルツハイマー病の分子機構解明に挑む--  [Invited]

  宮下尚之

  東北大学分子イメージング教育コース特別講義  2018/06  東北大学（仙台市）  東北大学CYRIC
  
• 機械学習を用いたテンプレートベースのタンパク質構造モデリング  [Not invited]

  古江祐也; 宮下尚之

  物理学会第７３回年次大会  2018/03  東京理科大学野田キャンパス（千葉県野田市）  日本物理学会
  
• モジュール型 CRISPRの核酸切断ダイナミクス  [Not invited]

  大橋燎; 宮下尚之

  物理学会第７３回年次大会  2018/03  東京理科大学野田キャンパス（千葉県野田市）  日本物理学会
  
• イオンの結合によるリボスイッチSPINACHの分子ダイナミクスへの影響  [Not invited]

  大西庸嵩; 古江祐也; 宮下尚之; 白木琢磨; 米澤康滋

  物理学会第７３回年次大会  2018/03  東京理科大学野田キャンパス（千葉県野田市）  日本物理学会
  
• 遺伝子編集タンパク質の改良に向けた分子シミュレーションを用いたプロトコル開発  [Not invited]

  高橋良太; 古江祐也; 梅田拓樹; 上野敦大; 米澤康滋; 宮下尚之

  第31回分子シミュレーション討論会  2017/11  石川県金沢市  分子シミュレーション研究会
  
• 薬剤の有無によるリボスイッチの構造変化  [Not invited]

  大西庸嵩; 古江祐也; 白木琢磨; 米澤康滋; 宮下尚之

  第31回分子シミュレーション討論会  2017/11  石川県金沢市  分子シミュレーション研究会
  
• 分子シミュレーションを用いた遺伝子編集タンパク質のデザイン  [Not invited]

  高橋良太; 古江祐也; 宮下尚之

  近畿大学大学院サイエンスネットワーク2017 第7回院生サミット  2017/09  奈良キャンパス(奈良市)  近畿大学
  
• 20aK-PS-52「ペプチドのリンカーによる構造揺らぎの抑制」  [Not invited]

  松井直人; 古江祐也; 宮下尚之; 瀧真清; 渡辺信一

  日本物理学会第72回年次大会(2017年)  2017/03  大阪府豊中市（大阪大学）  日本物理学会
  
• アルツハイマー病の初期分子機構と分子シミュレーション〜治療薬創薬に向けて〜  [Invited]

  宮下尚之

  第2回認知症高齢者の生活の質向上のための学際的シンポジウム  2017/03  東大阪（近畿大学）
• Molecular dynamics simulation of genome editing proteins toward the in silico design  [Not invited]

  Naoyuki Miyashita

  第3回「京」を中核とするHPCIシステム利用研究課題 成果報告会  2016/10  コクヨホール（東京品川）
• 生体分子シミュレーションと疾患機構 ～アルツハイマー病とコレステロール～  [Invited]

  宮下尚之

  バイオメクフォーラム２１研究会  2016/07  大阪大学基礎工学部シグマホール（国際棟） 

  近年、計算科学に関する技術の進歩によりコンピュータシステムの性能が劇的に上がってきた。この様なスーパーコンピュータをはじめとするコンピュータシステムを利用する事で、精度の高い様々な生体分子シミュレーションが可能になってきた。本講演では前半に最近のスーパーコンピュータの話をし、後半に講演者が行っている生体分子シミュレーションを用いたアルツハイマー病の分子機構に関する研究の紹介をする。
• Interaction between lipids and key protein for the early stage of AD  [Invited]

  Naoyuki Miyashita

  Structural dynamics of membrane proteins  2016/05
• コレステロールのアミロイド前駆体タンパク質（APP）二量体形成機構への影響  [Not invited]

  宮下尚之; 小串典子; 杉田有治

  日本物理学会 第71回年次大会（2016年）, 東北学院大学(仙台)  2016/03
• コレステロールとアミロイド前駆体タンパク質APPの相互作用  [Not invited]

  宮下尚之

  蛋白研セミナー 構造を基盤とする蛋白質科学における未解決問題  2016/03
• アルツハイマー病の初期分子機構 ～コレステロールとアミロイド前駆体タンパク質の二量体化～  [Invited]

  宮下尚之

  蛋白研セミナー 構造を基盤とする蛋白質科学における未解決問題, 東京大学先端科学研究センター（ENEOSホール）  2016/03
• Molecular simulation study of the molecular mechanism of early stage of Alzheimer disease.  [Invited]

  Naoyuki Miyashita

  The 6th Workshop on Computational and Statistical Physics  2015/11
• ガンやアルツハイマー病に関係する膜タンパク質の二量体構造予測とラフト環境における構造揺らぎ  [Not invited]

  宮下尚之

  ～スパコン「京」がひらく科学と社会～ 第2回「京」を中核とするHPCIシステム利用研究課題 成果報告会, 日本未来館（東京）  2015/10
• 疾患プロセスの詳細を生体分子シミュレーションで理解する〜アルツハイマー病の初期過程〜  [Invited]

  Naoyuki Miyashita

  私立大学戦略的研究基盤形成支援事業『地域・産学連携のためのライフイノベーション拠点形成』第1回成果評価会  2015/02  近畿大学生物理工学部（紀の川市）
• 熱安定型高活性TALENの開発  [Invited]

  Kazuho Ikeda; Naoyuki Miyashita

  バイオスーパーコンピューティングウインタースクール2015  2015/01
• 脂質分子とアミロイド前駆体タンパク質（APP）との相互作用とダイナミクス  [Invited]

  Naoyuki Miyashita

  神戸大学先端融合科学シンポジウム 『生体分子のダイナミクスを眺める』  2015/01  神戸大学大学院理学研究科
• TSUBAMEを用いた生体分子シミュレーション研究  [Invited]

  Naoyuki Miyashita

  GTC Japan 2014 (nVidia社), 東京ミッドタウンホール  2014/07
• 『REIN講習会』と演習 #3  [Invited]

  Naoyuki Miyashita

  「京」創薬支援アプリ(ISLiMソフトウエア)講習会  2014/02
• Coarse-Grained model simulation of amyloid precursor protein in a mixed lipid membrane system  [Not invited]

  Naoyuki Miyashita; Fumiko Ogushi; Yuji Sugita

  5th AICS International Symposium -Computer and Computational Sciences for Exascale, RIKEN AICS, Kobe, Japan  2014/01
• SIMULATION STUDY OF THE INTERACTION BETWEEN THE TRANSMEMBRANE REGION OF AMYLOID PRECURSOR PROTEIN AND LIPID  [Not invited]

  Naoyuki Miyashita; Fumiko Ogushi; Yuji Sugita

  新学術領域研究「動的秩序と機能」第2回国際シンポジウム（国際シンポジウム）・京都  2014/01
• The Simulation Study of the Interaction between Transmembrane Region of Amyloid Precursor Proteinj and Cholesterols  [Not invited]

  Naoyuki Miyashita; Fumiko Ogushi; Yuji Sugita

  4th AICS International Symposium -Computer and Computational Sciences for Exascale, RIKEN AICS, Kobe, Japan  2013/12
• The Interaction Between Transmembrane Region of Amyloid Precursor Protein (APP) and Cholesterols  [Not invited]

  Naoyuki Miyashita; Fumiko Ogushi; Yuji Sugita

  ICMS2013 (3rd International Conference on Molecular Simulation), Kobe, Japan  2013/11
• Interaction between cholesterols and the transmembrane region of Amyloid Precursor Protein.  [Not invited]

  Naoyuki Miyashita; Fumiko Ogushi; Yuji Sugita

  Workshop on Modeling Biomolecular Systems in Cellular Environments, Kyoto, Japan  2013/10
• アミロイド前駆体タンパク質(APP)の膜貫通領域とコレステロールとの相互作用  [Not invited]

  宮下尚之; 小串典子; 杉田有治

  日本物理学会講演概要集  2013/08
• Interaction Between Cholesterol And Transmembrane Region of Amyloid Precursor Protein(APP)  [Not invited]

  Miyashita Naoyuki; Ogushi Fumiko; Sugita Yuji

  Meeting abstracts of the Physical Society of Japan  2013/08
• The Structure of Amyloid Precursor Protein in The Membrane and The Development of Replica-exchange Interface Program (REIN)  [Not invited]

  Naoyuki Miyashita; Ogushi Fumiko; Yuji Sugita

  Membrane Protein Folding(Biophysical Society), Seoul, South Korea  2013/05
• 『REIN講習会』#2  [Invited]

  Naoyuki Miyashita

  「京」創薬支援アプリ(ISLiMソフトウエア)講習会  2013/03
• Replica-exchange interface  [Not invited]

  Naoyuki Miyashita

  3rd AICS International Symposium -Computer and Computational Sciences for Exascale, RIKEN AICS, Kobe, Japan  2013/03
• 『REIN講習会』#1  [Invited]

  Naoyuki Miyashita

  「京」創薬支援アプリ(ISLiMソフトウエア)講習会  2013/02
• コレステロールとAmyloid Precursor Protein(APP)の膜貫通部位との相互作用のシミュレーション研究  [Not invited]

  宮下尚之; 小串典子; 杉田有治

  日本分子生物学会年会プログラム・要旨集(Web)  2013
• レプリカ交換インターフェース(REIN)  [Not invited]

  宮下尚之; 李秀栄; 杉田有治

  分子シミュレーション討論会講演要旨集  2012/11
• KSHV免疫回避分子MIRによる免疫受容体の認識機構  [Not invited]

  梶川瑞穂; 青木雅美; LI Pai‐Chi; 水戸麻理; 宮下尚之; 杉田有治; 石戸聡

  日本ウイルス学会学術集会プログラム・抄録集  2012/10
• ミトコンドリアへの輸送蛋白質に付加されたプレ配列認識機構のレプリカ交換分子動力学計算  [Not invited]

  小室靖明; 森貴治; 宮下尚之; 宗行英朗; 齊藤貴士; 神田大輔; 杉田有治

  日本物理学会講演概要集  2012/03
• 27aPS-27 Recognition Mechanism of Presequence by Mitochondrial Outer Membrane Protein Tom20 using Replica-exchange Molecular Dynamics Simulation  [Not invited]

  Komuro Yasuaki; Mori Takaharu; Miyashita Naoyuki; Muneyuki Eiro; Saitoh Takashi; Kohda Daisuke; Sugita Yuji

  Meeting abstracts of the Physical Society of Japan  2012/03
• APPの膜近傍領域の構造と膜中での会合（二量体）構造予測  [Invited]

  Naoyuki Miyashita

  先端融合科学シンポジウム『タンパク質アセンブリ-会合、超分子化、凝集-』, 神戸大学  2012/01
• レプリカ交換分子動力学シミュレーションによる水中N型糖鎖の構造多様性とその調節機構の研究  [Not invited]

  二島渉; 宮下尚之; 山口芳樹; 杉田有治; 李秀栄

  分子シミュレーション討論会講演要旨集  2011/12
• ミトコンドリアへの輸送蛋白質に付加されたプレ配列認識モデルの分子動力学計算による検証  [Not invited]

  小室靖明; 森貴治; 宮下尚之; 宗行英朗; 齊藤貴士; 神田大輔; 杉田有治

  分子シミュレーション討論会講演要旨集  2011/12
• 多次元レプリカ交換インターフェース(REIN)の開発―アミロイド前駆体タンパク質の構造予測への応用―  [Not invited]

  宮下尚之

  日本物理学会講演概要集  2011/08
• 多次元レプリカ交換インターフェース(REIN)の開発‐‐レプリカ交換トンネリング時間の評価法(RETUNE)‐‐  [Not invited]

  宮下尚之; 杉田有治

  日本物理学会講演概要集  2011/08
• 23pGN-2 The development of multi-dimensional replica-exchange interface (REIN) : the structure prediction of APP  [Not invited]

  Miyashita Naoyuki

  Meeting abstracts of the Physical Society of Japan  2011/08
• 23aGN-8 The development of multi-dimensional replica-exchange interface (REIN) : the estimation of replica-exchange tunneling time (RETUNE)  [Not invited]

  Miyashita Naoyuki; Sugita Yuji

  Meeting abstracts of the Physical Society of Japan  2011/08
• The development of multi-dimensional replica-exchange interface (REIN) software and the estimation of simulation time of REMD  [Invited]

  Naoyuki Miyashita

  Korea-Japan Symposium on Statistical Mechanics Approaches to Nano/Bio-Science  2011/06
• カポジ肉腫関連ヘルペスウイルス免疫回避分子MIR2によるB7‐2認識の分子基盤  [Not invited]

  梶川瑞穂; 後藤栄治; LI Pai‐Chi; 宮下尚之; 青木(川住)雅美; 水戸(吉田)麻理; 杉田有治; 石戸聡

  日本蛋白質科学会年会プログラム・要旨集  2011/05
• LILR1/HLA‐GとLILR82/HLA‐G複合体の結合機構の違い  [Not invited]

  宮下尚之; 黒木喜美子; 前仲勝実; 杉田有治

  日本蛋白質科学会年会プログラム・要旨集  2010/05
• 分子シミュレーションによる蛋白質の分子認識機構とドラッグデザインへの可能性  [Not invited]

  杉田有治; 宮下尚之; 今井隆志

  日本薬学会年会要旨集  2010/03
• アミロイドβペプチドの生成に関するシミュレーション研究  [Not invited]

  宮下尚之; STRAUB John E; THIRUMALAI D; 杉田有治

  日本物理学会講演概要集  2010/03
• 21aEF-12 The Structure Prediction of APP Dimer and Monomer  [Not invited]

  Miyashita Naoyuki; Straub John E; Thirumalai D; Sugita Yuji

  Meeting abstracts of the Physical Society of Japan  2010/03
• Simulation studies on the differences in the binding mechanism of LILRB1/HLA-G and LILRB2/HLA-G  [Not invited]

  N. Miyashita; M. Maenaka; Y. Sugita

  Algorithms in MacroMolecular Modeling Conference, Austin,Texas, USA  2009/11
• 拡張アンサンブル法によるアミロイド前駆体蛋白質の膜中での二量体化構造予測  [Invited]

  Naoyuki Miyashita

  蛋白質研究所セミナー「蛋白質のバイオスーパーコンピューティング」大阪大学  2009/03
• Dimer conformation of amyloid precursor protein fragments in the membrane  [Not invited]

  Naoyuki Miyashita; John E. Straub; D. Thirumalai; Yuji Sugita

  Biophysical Society 53rd Annual Meeting, Boston, MA, USA  2009/03
• The structure prediction of APP dimmer in the membrane  [Invited]

  Naoyuki Miyashita; John E. Straub; Yuji Sugita

  Noise in complex systems, From molecular dynamics to stochastic modeling WORKSHOP 2008, Daejon, Korea  2008/05
• 変性剤中でのプリオン蛋白質の変性の初動機構  [Not invited]

  宮下尚之; 桑田一夫

  日本物理学会講演概要集  2008/02
• 25pPSB-47 Initial denaturation mechanism of PrPc in GdmCl.  [Not invited]

  Miyashita Naoyuki; Kuwata Kazuo

  Meeting abstracts of the Physical Society of Japan  2008/02
• アルツハイマー病に関わる膜蛋白質APPの膜貫通部位の二量体構造予測  [Not invited]

  宮下尚之; STRAUB John E; 杉田有治

  分子シミュレーション討論会講演要旨集  2008
• 3P018 The Structure of Amyloid β Peptide 1-40 in the membrane and the 672-726 fragment of of APP(Proteins-structure and structure-function relationship,Poster Presentations)  [Not invited]

  Miyashita Naoyuki; Straub John E; Devarajan Thirumalai

  Biophysics  2007/11
• 1P105 The function of the proton-counter transport in Ca^<2+>ATPase of sarcoplasmic reticulm  [Not invited]

  Miyashita N; Sugita Y; Ikeguchi M; Toyoshima C

  Biophysics  2004/11
• 29pWE-10 The function of the proton-counter transport in Ca^<2+> ATPase of sarcoplasmic reticulm  [Not invited]

  Miyashita Naoyuki; Sugita Yuji; Ikeguchi Mitsunori; Toyoshima Chikashi

  Meeting abstracts of the Physical Society of Japan  2004/03
• Competition between I-I solitons and N-I domain walls in photoinduced ionic-to neutral phase transition : Excitation intensity and degree of initial lattice disorder dependability  [Not invited]

  Miyashita Naoyuki; Yonemitsu Kenji

  Meeting abstracts of the Physical Society of Japan  2003/03
• Dimerization disordering and coupled charge-lattice dynamics after photoexcitations in a one-dimensional extended Peierls-Hubbard model.  [Not invited]

  Miyashita Naoyuki; Kuwabara Makoto; Yonemitsu Kenji

  Meeting abstracts of the Physical Society of Japan  2002/08
• Quantum Fluctuations and Coherence Recovery in the Photoinduccd Charge-Density-Wave-to-Charge-Polarization Phase Transition in MMX-Chain Compounds  [Not invited]

  Yonemitsu Kenji; Miyashita Naoyuki; Kuwabara Makoto

  Meeting abstracts of the Physical Society of Japan  2002/08
• 24aYD-13 Domain dynamics after photoexcitations in a one-dimensional Peierls-Hubbard model II.  [Not invited]

  Miyashita Naoyuki; Kuwabara Makoto; Yonemitsu Kenji

  Meeting abstracts of the Physical Society of Japan  2002/03
• Domain dynamics after photoexcitations in a one-dimensional Peierls-Hubbard model  [Not invited]

  Miyashita Naoyuki; Kuwabara Makoto; Yonemitsu Kenji

  Meeting abstracts of the Physical Society of Japan  2001/09
• イオン化いき則に於けるポテンシャルの形状と量子効果  [Not invited]

  宮下尚之; 加藤太治; 渡辺信一; 松沢通生

  日本物理学会講演概要集  1999/03
• 29p-ZC-7 Quantum effects and the role of the potential ridge in ionization threshold laws.  [Not invited]

  Miyashita Naoyuki; Kato Daiji; Watanabe Shinichi; Matsuzawa Michio

  Meeting abstracts of the Physical Society of Japan  1999/03

MISC

• DFHBIの有無によるリボスイッチSPINACH中のイオンの動力学への影響

  松倉里紗; 大西庸嵩; 古江祐也; 宮下尚之; 白木琢磨; 米澤康滋  日本物理学会講演概要集(CD-ROM)  74-  (2)  2019
• Dynamics of the gate of DFHBI and ions in riboswitch SPINACH

  Naoyuki Miyashita; Nobutaka Onishi; Masaya Furue; Takuma Shiraki; Yasushige Yonezawa  ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY  256-  2018/08
• Raft environments assist the aggregation of the transmembrane region of Amyloid Precursor Protein

  Naoyuki Miyashita; Fumiko Ogushi; Yuji Sugita  ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY  249-  2015/03
• 膜貫通型E3ユビキチンリガーゼMIRファミリーによる基質認識

  KAJIKAWA MIZUHO; LI PAI-CHI; KIMURA MINAKO; AOKI(KAWASUMI) MASAMI; MITO MARI; MIYASHITA NAOYUKI; SUGITA YUJI; ISHIDO SATOSHI  日本分子生物学会年会プログラム・要旨集(Web)  37th-  WEB ONLY 1P-0393  2014
• Interaction Between Cholesterol And Transmembrane Region of Amyloid Precursor Protein(APP)

  Miyashita Naoyuki; Ogushi Fumiko; Sugita Yuji  Meeting abstracts of the Physical Society of Japan  68-  (2)  317  -317  2013/08
• KSHV免疫回避分子MIRによる免疫受容体の認識機構

  KAJIKAWA MIZUHO; AOKI MASAMI; LI PAI-CHI; MITO MARI; MIYASHITA NAOYUKI; SUGITA YUJI; ISHIDO SATOSHI  日本ウイルス学会学術集会プログラム・抄録集  60th-  178  2012/10
• 27aPS-27 Recognition Mechanism of Presequence by Mitochondrial Outer Membrane Protein Tom20 using Replica-exchange Molecular Dynamics Simulation

  Komuro Yasuaki; Mori Takaharu; Miyashita Naoyuki; Muneyuki Eiro; Saitoh Takashi; Kohda Daisuke; Sugita Yuji  Meeting abstracts of the Physical Society of Japan  67-  (1)  429  -429  2012/03
• Modulation Mechanism on the Conformational Diversities of Biantennary Complex-Type N-Glycans in Water

  Wataru Nishima; Naoyuki Miyashita; Yoshiyuki Yamaguchi; Yiji Sugita; Suyong Re  BIOPHYSICAL JOURNAL  102-  (3)  736A  -737A  2012/01
• 23aGN-8 The development of multi-dimensional replica-exchange interface (REIN) : the estimation of replica-exchange tunneling time (RETUNE)

  Miyashita Naoyuki; Sugita Yuji  Meeting abstracts of the Physical Society of Japan  66-  (2)  324  -324  2011/08
• 23pGN-2 The development of multi-dimensional replica-exchange interface (REIN) : the structure prediction of APP

  Miyashita Naoyuki  Meeting abstracts of the Physical Society of Japan  66-  (2)  332  -332  2011/08
• カポジ肉腫関連ヘルペスウイルス免疫回避分子MIR2によるB7‐2認識の分子基盤

  KAJIKAWA MIZUHO; GOTO EIJI; LI PAI-CHI; MIYASHITA NAOYUKI; AOKI(KAWASUMI) MASAMI; MITO(YOSHIDA) MARI; SUGITA YUJI; ISHIDO SATOSHI  日本蛋白質科学会年会プログラム・要旨集  11th-  67  2011/05
• LILR1/HLA‐GとLILR82/HLA‐G複合体の結合機構の違い

  宮下尚之; 黒木喜美子; 前仲勝実; 杉田有治  日本蛋白質科学会年会プログラム・要旨集  10th-  66  2010/05
• 21aEF-12 The Structure Prediction of APP Dimer and Monomer

  Miyashita Naoyuki; Straub John E.; Thirumalai D.; Sugita Yuji  Meeting abstracts of the Physical Society of Japan  65-  (1)  383  -383  2010/03
• Probing the principles governing protein aggregation

  John E. Straub; Eva K. Rivera; Susan C. DeSensi; Naoyuki Miyashita; D. Thirumalai  ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY  238-  2009/08
• 25pPSB-47 Initial denaturation mechanism of PrPc in GdmCl.

  Miyashita Naoyuki; Kuwata Kazuo  Meeting abstracts of the Physical Society of Japan  63-  (1)  382  -382  2008/02
• 29pWE-10 The function of the proton-counter transport in Ca^<2+> ATPase of sarcoplasmic reticulm

  Miyashita Naoyuki; Sugita Yuji; Ikeguchi Mitsunori; Toyoshima Chikashi  Meeting abstracts of the Physical Society of Japan  59-  (1)  376  -376  2004/03
• Electronic and lattice dynamics in the photoinduced ionic-to-neutral phase transition in a one-dimensional extended Peierls-Hubbard model

  N Miyashita; M Kuwabara; K Yonemitsu  JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN  72-  (9)  2282  -2290  2003/09
• Competition between I-I solitons and N-I domain walls in photoinduced ionic-to neutral phase transition : Excitation intensity and degree of initial lattice disorder dependability

  Miyashita Naoyuki; Yonemitsu Kenji  Meeting abstracts of the Physical Society of Japan  58-  (1)  676  -676  2003/03
• Dimerization disordering and coupled charge-lattice dynamics after photoexcitations in a one-dimensional extended Peierls-Hubbard model.

  Miyashita Naoyuki; Kuwabara Makoto; Yonemitsu Kenji  Meeting abstracts of the Physical Society of Japan  57-  (2)  644  -644  2002/08
• Quantum Fluctuations and Coherence Recovery in the Photoinduccd Charge-Density-Wave-to-Charge-Polarization Phase Transition in MMX-Chain Compounds

  Yonemitsu Kenji; Miyashita Naoyuki; Kuwabara Makoto  Meeting abstracts of the Physical Society of Japan  57-  (2)  709  -709  2002/08
• 24aYD-13 Domain dynamics after photoexcitations in a one-dimensional Peierls-Hubbard model II.

  Miyashita Naoyuki; Kuwabara Makoto; Yonemitsu Kenji  Meeting abstracts of the Physical Society of Japan  57-  (1)  663  -663  2002/03
• Domain dynamics after photoexcitations in a one-dimensional Peierls-Hubbard model

  Miyashita Naoyuki; Kuwabara Makoto; Yonemitsu Kenji  Meeting abstracts of the Physical Society of Japan  56-  (2)  610  -610  2001/09
• 29p-ZC-7 Quantum effects and the role of the potential ridge in ionization threshold laws.

  Miyashita Naoyuki; Kato Daiji; Watanabe Shinichi; Matsuzawa Michio  Meeting abstracts of the Physical Society of Japan  54-  (1)  754  -754  1999/03

Research Grants & Projects

• フラビウイルス科の各ウイルスを厳密に区別できるモノクローナル抗体の開発

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)

  Date (from‐to) : 2021/04 -2024/03 

  Author : 加藤 龍一; 小澤 龍彦; 正木 秀幸; 宮下 尚之

   

  ウエストナイルウイルス（WNV）は、時に致死性の脳炎・髄膜炎を惹き起こすフラビウイルス科の蚊媒介性ヒト感染性ウイルスである。世界の広い地域に分布し我が国への感染拡大の危険性が指摘されているが、実用的な治療薬やワクチンは未だ無い。研究分担者らによって見出された WNV に働く中和抗体は、同じフラビウイルス科の日本脳炎ウイルス(JEV)とも交差反応を示すという興味深い性質を持つ。我々はその抗体と WNV のエンベロープタンパク質（Ｅタンパク質）との複合体の立体構造の決定に成功し、異なるウイルスを同時に認識する抗体の分子機構を明らかにした。その構造基盤を発展させ、(1) フラビウイルス科の各種ウイルスを同時に認識する抗体を開発し、異なるフラビウイルス感染症のどれにも効果のある抗体医薬開発につながる知見を得ること、(2) フラビウイルス科の中の特定のウイルスだけを認識する抗体を開発し、多重感染地域などでどのウイルスに感染しているかを判定できる診断薬の開発につながる知見を得ること、を研究の目的とし、フラビウイルス科の日本脳炎、黄熱病、ジカ熱の各ウイルス（JEV, YFV, ZIKV）のＥタンパク質とその中和抗体の認識機構を明らかにすべく、両者のタンパク質複合体の立体構造解析を目指し研究を行った。
• 血液凝固機能を阻害する非天然型DNAアプタマー薬剤の構造とヌクレアーゼ耐性機構

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)

  Date (from‐to) : 2021/04 -2024/03 

  Author : 渡辺 信一; 瀧 真清; 山越 智健; 宮下 尚之

   

  TBAは天然の４種の核酸の中のTとGのみで形成され、塩基配列は5'-GGTTGGTGTGGTTGG-3'である。４つのグアニン対を持ち、２つの対の各々が安定なグアニン４重鎖と呼ばれる平面構造（G-plate、G-quadruplex）を形成する。２つの平面が並行なチューブ状に並び、その中にK+イオンを捕獲するイオンチャネルを形成すると堅固なDNAアプタマーとなる。G-plateによる堅固な構造は生体内では染色体の末端部にあるテロメアにも見られ、癌の抑制/惹起の研究でも興味を持たれている。本研究はこの興味深いDNAアプタマーの(a)構造と安定性、(b)ヌクレアーゼ耐性、(c)特異的結合能点を考察する。また、共同研究者らから動力学の分析に有効な数理手法やTBAに関連するDNAアプタマーの実験的研究の情報を得ながら研究を進めている。 全体像を得るために特に重要なものは(a)である。TBAだけではなく、類似の構造で性質の異なるものの比較が必要である。実験的先行研究では、幾つかの核酸をα-アノマーで置き換えているが、アノマーの実験的・理論的構造決定はできていない。MD計算をするため、山越と渡辺はxleapを利用し、宮下はpythonツールを開発して、アノマー化したTBAのpdbを作った。塩基を糖との軸について回転させてsynとantiの配置による安定性の吟味もMDシミュレーションで実施したが、これらの試行的な結果はまだ発表の段階に至っていない。 本研究の目的(b)に関して、瀧はTBAにターゲットと共有結合するwarheadを付けたDNA・コバレント・アプタマー(TBDcA)を実験的に作成し、その各種ヌクレアーゼ耐性機構を検討し、有意な結果を得た。宮下はTBDcAの理論計算の前段階としてペプチドをベースにしたペプチド・コバレント・アプタマー（PecA）の知見を得る準備研究を実施した。
• 分子シミュレーションを用いたアルツハイマー病におけるAβ産生の起点機構の詳細解明

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)

  Date (from‐to) : 2021/04 -2024/03 

  Author : 宮下 尚之

   

  アルツハイマー病の初期過程における分子機構では、ニューロン細胞にある膜タンパク質であるアミロイド前駆体タンパク質（APP）が通常では膜タンパク質のα切断酵素によって切断されるところが、膜タンパク質のβ切断酵素によって切断されC-APPが生成される。その後、γ切断酵素によって切断され、アミロイドβペプチドが産生される。本研究では、分子シミュレーションを用いたアルツハイマー病におけるAβ産生の起点機構の詳細解明における、特にβ切断酵素とAPPとの特異的な動的相互作用の観点から研究を進めている。 我々のこれまでの研究から、生体分子の相互作用には特異的な動的相互作用があることに気づいた。これは例えば膜タンパク質間の相互作用の際にはコレステロールなどの脂質分子が相互作用に関わってきたりする。これまでの研究では膜貫通部位のみの動力学を考慮していたが、本研究では全長を考える点が新しい点である。本研究はβ切断酵素とAPP、α切断酵素とAPPとの相互作用の研究であるが、このようなアルツハイマー病の起点現象を通して、膜タンパク質間相互作用の知見を深めることにつなげようとしている。 本年度成果としては、１）β切断酵素の全長構造のモデリングを実施し、２）その全原子モデル分子動力学（MD）シミュレーションを実施した。その結果、細胞外領域にあるβ切断酵素の切断部位の運動には制限があり、β切断酵素とAPPとの結合過程が切断に影響することがわかってきた。
• 進化工学的および分子動力学的手法による新規ゲノム編集システムの創出 (NEDOスマートセルプロジェクト）

  NEDO：「植物等の生物を用いた高機能品生産技術の開発/ 研究開発項目1 植物の生産性制御に係る共通基盤技術開発」

  Date (from‐to) : 2019/04 -2021/03 

  Author : Naoyuki Miyashita
• 分子シミュレーションによるアルツハイマー病初期分子機構への生体膜環境の影響解析

  文部科学省：科学研究費補助金(基盤研究(C))

  Date (from‐to) : 2017/04 -2020/03 

  Author : 宮下尚之
• 再委託：進化工学的および分子動力学的手法による新規ゲノム編集システムの創出 (NEDOスマートセルプロジェクト）

  NEDO・理化学研究所（再委託）：再委託・NEDO

  Date (from‐to) : 2016/09 -2019/03 

  Author : 刑部敬史; 再委託; 理研から; 宮下尚之
• 2-(2)-2 構造解析と分子動力学計算を用いた合理的分子設計によるゲノム編集酵素の改良

  内閣府：戦略イノベーション創造プログラム（SIP）次世代農林水産業創造技術『ゲノム編集技術と開花促進技術の基盤技術の確立と高度化（生研）』

  Date (from‐to) : 2014/10 -2019/03 

  Author : Yasushi Okada; 分担; Takanori Kigawa; Naoyuki Miyashita
• Development of the program module for the docking between gamma-secretase and APP

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 2014 -2016 

  Author : MIYASHITA Naoyuki; TAKAJI Tatsuya

   

  We have developed the program module that is finding the docking interface between large membrane protein and small membrane protein. It is the module in REIN program. We had code it to find the docking interface between a gamma-secretase and a amyloid precursor protein (APP). ①We developed a program module using NAMD. ② We also performed the simulation of a wild type gamma-secretase and a mutant gannma-secretase. The motion of the protein of the mutant was totally different from the wild type. We could get a new insight for gamma-secretase's dynamics. ③ We used the new module for the docking simulation between the gamma-secretase and APP. We are doing more detail analysis now.
• Interaction between membrane protein and lipids in the raft

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 2012 -2013 

  Author : NAOYUKI Miyashita

   

  Bio-membrane consists of membrane proteins and a various variety of lipids. Nano-domains that are called "Raft" are created in such heterogeneous system. The raft contains a lot of cholesterols and Sphingo-lipids. The functions of Amyloid Precursor Proteins (APP), are related to the Alzheimer disease, are affected by the raft. We have investigated the interaction between lipid and APP, and the interaction of membrane proteins in the raft. Our results suggested that the cholesterols are collected around the APP, especially Gly-xxx-Gly motif, and the cholesterols assist the association of APP.

Teaching Experience

Statistical Physics for biomolecularStatistical Physics for biomolecular Kindai University

Social Contribution

• シンポジウム『The function and mechanism of intramolecular information-transmission in protein』

  Date (from-to) : 2018/09/15-2018/09/15

  Role : Presenter

  Category : Seminar

  Sponser, Organizer, Publisher  : 日本生物物理学会年会

  Event, Program, Title : 第５６回日本生物物理学会年会

  岡山大学（岡山市）
• 研究室公開『スーパーコンピュータで見た生体分子』

  Date (from-to) : 2018/09/02-2018/09/02

  Role : Lecturer

  Category : Open college

  Sponser, Organizer, Publisher  : 近畿大学生物理工学部

  Event, Program, Title : 近畿大学生物理工学部オープンキャンパス

  近畿大学生物理工学部
• 『きのくに科学オリンピック 科学力向上ゼミ 情報（高校生対象）』

  Date (from-to) : 2018/08/10-2018/08/10

  Role : Lecturer

  Category : Qualification seminar

  Sponser, Organizer, Publisher  : 和歌山県

  Event, Program, Title : 『きのくに科学オリンピック 科学力向上ゼミ 情報（高校生対象）』

  High school students 近畿大学生物理工学部
• ワークショップ『タンパク質の分子内情報伝達機構研究の新展開』

  Date (from-to) : 2018/06/28-2018/06/28

  Role : Presenter

  Category : Seminar

  Sponser, Organizer, Publisher  : 日本蛋白質科学会年会

  Event, Program, Title : 第１８回日本蛋白質科学会年会

  新潟市
• シンポジウム『HPCシステムを使った生命科学 ― 分子スケールから細胞に向けて ―』

  Date (from-to) : 2018/03/13-2018/03/13

  Role : Presenter

  Category : Seminar

  Sponser, Organizer, Publisher  : 近畿大学生物理工学部

  Event, Program, Title : 第１回近畿大学生物理工学部HPCシンポジウム

  近畿大学生物理工学部（紀の川市）
• BOST Science Cafe 『近未来産業のための新しい生体なのツールのしくみ〜遺伝子編集システムのシミュレーション〜』

  Date (from-to) : 2017/09/23-2017/09/23

  Role : Lecturer

  Category : Lecture

  Sponser, Organizer, Publisher  : 和歌山県教育委員会・橋本市教育委員会

  Event, Program, Title : 平成２９年度第６回近畿大学生物理工学部公開講座

  橋本商工会館（和歌山県橋本市）
• 模擬講義 『ミクロの世界の認知症〜スーパーコンピュータを活用する〜』

  Date (from-to) : 2017/09/05-2017/09/05

  Role : Lecturer

  Category : Visiting lecture

  Sponser, Organizer, Publisher  : 近畿大学付属高校

  Event, Program, Title : 近畿大学附属高等学校模擬講義

  近畿大学附属高等学校（大阪府東大阪市
• 研究室実験室公開 『ナノサイズの生体分子の動きを３DやVRで見よう

  Date (from-to) : 2017/08/27-2017/08/27

  Role : Lecturer

  Category : Open college

  Sponser, Organizer, Publisher  : 近畿大学生物理工学部

  Event, Program, Title : 近畿大学生物理工学部オープンキャンパス

  近畿大学生物理工学部（和歌山県紀の川市）
• 向陽高校 研究室公開『ナノサイズの生体分子の動きを３DやVRで見よう』

  Date (from-to) : 2017/08/24-2017/08/24

  Role : Lecturer

  Category : Open college

  Sponser, Organizer, Publisher  : 近畿大学生物理工学部

  Event, Program, Title : 和歌山県立向陽高等学校SSH生物理工学部見学会

  High school students 近畿大学生物理工学部（和歌山県紀の川市）
• 体験イベント 生物理工学部の世界『ナノサイズの生体分子の動きを３DやVRで見よう』

  Date (from-to) : 2017/08/19-2017/08/19

  Role : Lecturer

  Category : Open college

  Sponser, Organizer, Publisher  : 近畿大学

  Event, Program, Title : 近畿大学オープンキャンパス

  近畿大学東大阪キャンパス（大阪府東大阪市）
• スーパーコンピュータを作ろう(近大付属和歌山見学会)

  Date (from-to) : 2017/07/30-2017/07/30

  Role : Lecturer

  Category : Open college

  Sponser, Organizer, Publisher  : 近畿大学生物理工学部

  Event, Program, Title : 近畿大学附属和歌山高等学校 オープンキャンパス内見学会

  High school students 和歌山県紀の川市
• 体験学習 『スーパーコンピュータを作ろう』

  Date (from-to) : 2017/07/30-2017/07/30

  Role : Lecturer

  Category : Open college

  Sponser, Organizer, Publisher  : 近畿大学生物理工学部

  Event, Program, Title : 近畿大学生物理工学部オープンキャンパス

  近畿大学生物理工学部(紀の川市)
• 『情報科学とアルゴリズム』

  Date (from-to) : 2017/07/22-2017/07/22

  Role : Lecturer

  Category : Seminar

  Sponser, Organizer, Publisher  : 和歌山県教育委員会主催

  Event, Program, Title : きのくに科学オリンピック 科学向上ゼミ2017〜情報〜

  High school students 近畿大学生物理工学部キャンパス（紀の川市）
• Dementia from a nano world

  Date (from-to) : 2016/06/25-2016/06/25

  Role : Lecturer

  Category : Lecture

  Sponser, Organizer, Publisher  : BOST KNDAI University

  Event, Program, Title : 第４回 生物理工学部公開講座
• 模擬講義「生命科学とコンピュータ」

  Date (from-to) : 2015/11/09-2015/11/09

  Role : Lecturer

  Category : Visiting lecture

  Sponser, Organizer, Publisher  : 桜宮高校

  High school students 桜宮高校（大阪）
• 『 3Dで生体分子の立体構造を見よう--3D顕微鏡?!--』

  Date (from-to) : 2015/09/27-2015/09/27

  Role : Demonstrator

  Category : Open college

  Sponser, Organizer, Publisher  : 近畿大学

  Event, Program, Title : 近畿大学オープンキャンパス BOST World

  近畿大学本部キャンパス

Media Coverage

• 「ボックス！」

  Date : 2020/12/01

  Writer: Myself

  Publisher, broadcasting station: 和歌山放送

  Program, newspaper magazine: 「ボックス！」

  Media report
• 近畿大学生物理工学部ラジオ講座～身近な科学～

  Date : 2016/04/19

  Publisher, broadcasting station: 近畿大学生物理工学部

  Program, newspaper magazine: 和歌山放送ラジオ「ボックス」

  Media report

Others

• 2019/04 -2019/04  深層学習を用いた医療カルテ情報からの疾患予測プログラム開発 

  平成３１年度近畿大学生物理工学部戦略研究 １８ーIII-23 経費：333千円
• 2018/04 -2018/04  分子シミュレーションとDeep Learningを組み合わせたタンパク質立体構造モデリングプログラムの開発 

  平成３０年度近畿大学生物理工学部戦略的研究 17'－I－1 経費：3,000千円 共同研究者：根本充貴
• 2017/04 -2017/04  安価なアルツハイマー治療薬の設計を目指した、リンカーペプチド・アプタマー薬剤のデザインの指針を得るための構造予測シミュレーション研究 

  平成29年度近畿大学生物理工学部 戦略的研究 16-III-24 経費400千円
• 2016/04 -2016/04  アルツハイマー病治療薬創薬に向けたγ切断酵素のアミノ酸変異に関する生体分子シミュレーション研究 

  平成２８年度近畿大学生物理工学部 戦略的研究 15-I-1 経費3,000千円 研究組織： システム生命科学科：木村裕一 先端技術総合研究所：米澤康滋
• 2016/04 -2016/04  タンパク質構造予測用の超小型省電力並列計算機システムの構築を通した、生物系の学生のためのハイパフォーマンスコンピューティング(HPC)教育の試行 

  近畿大学学内研究助成金 21 世紀教育開発奨励金（教育推進研究助成金） KS04 経費1,000千円 研究内容 近畿大学生物理工学部の希望する学生と共に超小型省電力PCを並列に結合した超小型クラスターPCを作成し、ハイブリッド並列プログラミングを体験してもらう。また、多次元レプリカ交換インターフェースプログラム(replica-exchange interface program): REIN を使った生体分子構造予測計算を学生と共に実施する。 成果関連論文："On-the-fly analysis of molecular dynamics simulation trajectories of proteins using the Bayesian inference method" 宮下尚之, 米澤康滋 The Journal of Chemical Physics 147 124108-1-124108-8 2017年9月

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researchmap

https://researchmap.jp/yukimya