KINDAI UNIVERSITY


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MIYASHITA Naoyuki

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FacultyDepartment of Computational Systems Biology / Graduate School of Biology-Oriented Science and Technology
PositionAssociate Professor
Degree
Commentator Guidehttps://www.kindai.ac.jp/meikan/1352-miyashita-naoyuki.html
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Last Updated :2020/09/30

Education and Career

Education

  •   1992 04  - 1997 03 , University of Electro-Communications, Department of Electro-Communications
  •   1997 04  - 1999 03 , University of Electro-Communications, Department of Electro-Communications
  •   1999 04  - 2003 03 , The Graduage University for Advanced Study

Academic & Professional Experience

  •   2018 04 ,  - 現在, Visiting Associate Professor, University of Electro-Communicatins
  •   2018 04 ,  - 現在, Visiting Scientist, RIKEN Center for Biosystems Dynamics Research
  •   2017 04 ,  - 現在, Associate Professor, Biology Oriented Science & Technology, KINDAI University
  •   2016 04 ,  - 現在, Kindai University
  •   2015 08 ,  - 現在, Visiting Scientists, RIKEN AICS
  •   2015 04 ,  - 2018 03 , Visiting Scientist, RIKEN QBiC
  •   2015 04 ,  - 2017 03 , Associate Professor, Biology Oriented Science & Technology, KINDAI University
  •   2011 04 ,  - 2015 03 , Research Scientist, AICS, RIKEN
  •   2011 04 ,  - 2015 03 , Research Scientist, QBiC, RIKEN
  •   2013 07 ,  - 2013 07 , 非常勤講師, 理学研究科, Kobe University
  •   2011 04 ,  - 2013 03 , Research Scientist, ISLiM, RIKEN
  •   2007 12 ,  - 2011 03 , Research Scientist, ISLiM, RIKEN
  •   2007 04 ,  - 2007 11 , Assistant Professor, CEID, GIFU University
  •   2005 04 ,  - 2007 03 , Research Associate, Chemistry Department, BOSTON University
  •   2003 04 ,  - 2005 03 , Post Doctoral fellow, IMCB, The University of Tokyo
  •   2001 06 ,  - 2003 02 , RA, 岡崎国立共同研究機構

Research Activities

Research Areas

  • Informatics, Biological, health, and medical informatics
  • Informatics, Biological, health, and medical informatics

Research Interests

  • APP, replica-exchange

Published Papers

  • 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), Journal of immunology (Baltimore, Md. : 1950), 203(12), 3386 - 3394, Dec. 15 2019 , Refereed
    Summary: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.
  • 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, BIOPHYSICAL JOURNAL, 104(2), 665A, Jan. 29 2013 , Refereed
  • Recent Applications of Replica-Exchange Molecular Dynamics Simulations of Biomolecules, Yuji Sugita, Naoyuki Miyashita, Pai-Chi Li, Takao Yoda, Yuko Okamoto, Current Physical Chemistry, Current Physical Chemistry, 2(4), 401 - 412, Dec. 2012 , Refereed
  • The inter-transmembrane region of KSHV MIR2 contributes to B7-2 own regulation, M. Kajikawa, P.-C. Li, E. Goto, N. Miyashita, M. Aoki, M. Mito, S. Ishido, Y. Sugita, Journal of Virology, Journal of Virology, 86(9), 5288 - 5296, May 2012 , Refereed
  • Winter School 2011 for the Integrated Simulation of Living Matter, Y. Ishimine, H. Urakubo, Y. Sunaga, G. Masumoto, K. Misawa, N. Miyashita, BioSupercomputing Newsletter, BioSupercomputing Newsletter, 4, 11 - 11, 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), 情報処理学会研究報告(CD-ROM), 2010(4), ROMBUNNO.HPC-127,4, Dec. 2010 , Refereed
  • Structure prediction of APP fragments using Replica-exchange molecular dynamics simulation, Naoyuki Miyashita, Yuji Sugita, IPSJ SIG Notes, IPSJ SIG Notes, 2010(4), 1 - 6, Oct. 2010 , Refereed
    Summary: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.
  • Replica-exchange Molecular Dynamics Simulations of Amyloid Precursor Protein Dimer in Membran, Naoyuki Miyashita, Yuji Sugita, Quantum Bio-Informatics III From Quantum Information to Bio-Informatics, Quantum Bio-Informatics III From Quantum Information to Bio-Informatics, 361 - 368, Mar. 2010
  • Prediction of Transmembrane Dimer Structure of Amyloid Precursor Protein using Replica-Exchange Molecular Dynamics Simulations, Naoyuki Miyashita, Yuji Sugita, BioSupercomputing Newsletter, BioSupercomputing Newsletter, 1, 10 - 10, Oct. 2009
  • Influence of short-range interference on ionization threshold law, Naoyuki Miyashita, Shinichi Watanabe, Michio Matsuzawa, Joseph H. Macek, Physical Review A, Physical Review A, 61, 014901, Dec. 1999 , Refereed
  • 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, 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, Mar. 1999
  • On-the-fly analysis of molecular dynamics simulation trajectories of proteins using the Bayesian inference method, Naoyuki Miyashita, Yasushige Yonezawa, JOURNAL OF CHEMICAL PHYSICS, JOURNAL OF CHEMICAL PHYSICS, 147(12), 124108-1 - 124108-8, Sep. 2017 , Refereed
    Summary: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, BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1858(7), 1635 - 1651, Jul. 2016 , Refereed
    Summary: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.
  • REIN: Replica-Exchange INterface for Simulating Protein Dynamics and Function, Naoyuki Miyashita, Suyong Re, Yuji Sugita, INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 115(5), 325 - 332, Mar. 2015 , Refereed
    Summary: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, JOURNAL OF COMPUTATIONAL CHEMISTRY, 35(4), 300 - 308, Feb. 2014 , Refereed
    Summary: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.
  • 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, Journal of Physical Chemistry B, 117(10), 2864 - 2871, Mar. 14 2013 , Refereed
    Summary: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.
  • 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, JOURNAL OF PHYSICAL CHEMISTRY B, 116(29), 8504 - 8512, Jul. 2012 , Refereed
    Summary: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.
  • Conformational flexibility of N-glycans in solution studied by REMD simulations, Suyong Re, Wataru Nishima, Naoyuki Miyashita, Yuji Sugita, Biophysical Reviews, Biophysical Reviews, 4(3), 179 - 187, 2012 , Refereed
    Summary: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, BIOPHYSICAL JOURNAL, 101(10), L44 - L46, Nov. 2011 , Refereed
    Summary: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, JOURNAL OF PHYSICAL CHEMISTRY B, 115(25), 8288 - 8295, Jun. 2011 , Refereed
    Summary: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.
  • 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, MOLECULAR IMMUNOLOGY, 48(1-3), 314 - 320, Nov. 2010 , Refereed
    Summary: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
  • 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, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131(49), 17843 - 17852, Dec. 2009 , Refereed
    Summary: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.
  • 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, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131(10), 3438 - +, Mar. 2009 , Refereed
    Summary: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.
  • 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, BIOCHEMISTRY, 45(39), 11752 - 11761, Oct. 2006 , Refereed
    Summary: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, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102(41), 14489 - 14496, Oct. 2005 , Refereed
    Summary: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, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 127(17), 6150 - 6151, May 2005 , Refereed
  • 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, JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 72(9), 2282 - 2290, Sep. 2003 , Refereed
    Summary: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, PHYSICAL REVIEW B, 68(7), 075113(9), Aug. 2003 , Refereed
    Summary: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, SYNTHETIC METALS, 135(1-3), 645 - 646, Apr. 2003 , Refereed
    Summary: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, SYNTHETIC METALS, 135(1-3), 521 - 522, Apr. 2003 , Refereed
    Summary: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, PHASE TRANSITIONS, 75(7-8), 887 - 893, Oct. 2002 , Refereed
    Summary: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, MOLECULAR CRYSTALS AND LIQUID CRYSTALS, 379(1), 467 - 474, 2002 , Refereed
    Summary: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.
  • 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, Physical Review A - Atomic, Molecular, and Optical Physics, 59(6), 4385 - 4389, 1999 , Refereed
    Summary: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

  • Molecular dynamics simulations of CRISPR Cas3 and Cse1 complex, ◯Tomohiro Yamaguchi, Yui Taketomo, Naoyuki Miyashita,   2019 09 25
  • Development of Deep-Autoencoder based Homology Modeling software, ◯Masaya Furue, Mitsutaka Nemoto, Lisa Matsukura, Naoyuki Miyashita,   2019 09 25
  • Influence on the structure and dynamics of Riboswitch “SPINACH” and potassium ions by DFHBI, ◯Lisa Matsukura, Nobutaka Onishi, Masaya Furue, Naoyuki Miyashita, Takuma Shiraki, Yasushige Yonezawa,   2019 09 24
  • Interaction between amyloid precursor protein and beta-secretase in the bio-membrane, ◯Kaori Yanagino, Naoyuki Miyashita,   2019 09 24
  • Molecular Dynamics Simulation of CRISPR Cas3, ○Tomohiro Yamaguchi, Yui Takatomo, Naoyuki Miyashita,   2019 06 26
  • Structure Prediction of Transmembrane domain of beta-secretase, ◯Kaori Yanagino, Naoyuki Miyashita,   2019 06 24
  • Mechanism of the interaction between Hsp90 and the medium molecule drug, and the docking simulation, ○Lisa Matsukura, Kazuto Mochizuki, Masaya Furue, Masumi Taki, Naoyuki Miyashita,   2019 06 24
  • Development of Homology modeling program using Deep Learning, ○Masaya Furue, Lisa Matsukura, Mitsutaka Nemoto, Naoyuki Miyashita,   2019 06 24
  • Dynamics of CRISPR Cas System, ○Naoyuki Miyashita, Yui Taketomo, Tomohiro Yamaguchi, Lisa Matsukura, Ryo Ohashi,   2019 06 24
  • Molecular Dynamics Simulation of Module-Type CRISPR System, Naoyuki Miyashita, CCS International Symposium 2018 10th symposium on Discovery, Fusion, Creation of New Knowledge by Multidisciplinary Computational Sciences,   2018 10 15 , Tsukuba University
  • Development of Template-Based Protein Structure Modeling Method Using Deep-Autoencoder with a Denoising Algorithm, Masaya Furue, Mitsutaka Nemoto, Naoyuki Miyashita,   2018 10 09
  • Microsecond Molecular Dynamics Simulations of Medium Molecule Drugs and the docking with a target protein, Lisa Matsukura, Kazuto Mochizuki, Masumi Taki, Shinichi Watanabe, Naoyuki Miyashita,   2018 10 09
  • The dynamics of CRISPR-CMR before/after the cleavage of targeted RNA, ○Tomohiro Yamaguchi, Ryo Ohashi, Naoyuki Miyashita,   2018 09 16
  • Dynamics of the cleavage of DNA/RNA in module type CRISPR/CAS system by using molecular dynamics, Naoyuki Miyashita, Ryo Ohashi, Reiwat Takeuchi, Yui Taketomo,   2018 09 16
  • Dynamics of peptide aptamer which targeting Hsp90 and the development of supporting program for modification of force field parameters, ○Lisa Matsukura, Kazuto Mochizuki, Masumi Taki, Naoyuki Miyashita,   2018 09 15
  • Development of Template-based Protein Structure Modeling Software using Molecular Dynamics Simulations of Template proteins., Masaya Furue, Mitsutaka Nemoto, Naoyuki Miyashita,   2018 09 15
  • Dynamics of the gate of DFHBI and Ions in riboswitch SPINACH, Naoyuki Miyashita, Nobutaka Onishi, Masaya Furue, Takuma Shiraki, Yasushige Yonezawa, The 256th ACS National Meeting (アメリカ化学会),   2018 08 21
  • Molecular dynamics simulation of genome editing proteins toward the in silico design, Naoyuki Miyashita,   2016 10 21
  • Interaction between lipids and key protein for the early stage of AD, Naoyuki Miyashita, Structural dynamics of membrane proteins,   2016 05 13 , 招待有り
  • Molecular simulation study of the molecular mechanism of early stage of Alzheimer disease., Naoyuki Miyashita, The 6th Workshop on Computational and Statistical Physics,   2015 11 21 , 招待有り
  • 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〜, 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 27 , 招待有り
  • 熱安定型高活性TALENの開発, 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 31 , 招待有り
  • 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, 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 19 , 招待有り
  • TSUBAMEを用いた生体分子シミュレーション研究, Naoyuki Miyashita, GTC Japan 2014 (nVidia社), 東京ミッドタウンホール,   2014 07 , 招待有り
  • 『REIN講習会』と演習 #3, Naoyuki Miyashita, 「京」創薬支援アプリ(ISLiMソフトウエア)講習会,   2014 02 , 招待有り
  • Coarse-Grained model simulation of amyloid precursor protein in a mixed lipid membrane system, 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, 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, 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, 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., 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, 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 26
  • 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,   2013 08 26
  • The Structure of Amyloid Precursor Protein in The Membrane and The Development of Replica-exchange Interface Program (REIN), Naoyuki Miyashita, Ogushi Fumiko, Yuji Sugita, Membrane Protein Folding(Biophysical Society), Seoul, South Korea,   2013 05
  • 『REIN講習会』#2, Naoyuki Miyashita, 「京」創薬支援アプリ(ISLiMソフトウエア)講習会,   2013 03 , 招待有り
  • Replica-exchange interface, Naoyuki Miyashita, 3rd AICS International Symposium -Computer and Computational Sciences for Exascale, RIKEN AICS, Kobe, Japan,   2013 03
  • 『REIN講習会』#1, Naoyuki Miyashita, 「京」創薬支援アプリ(ISLiMソフトウエア)講習会,   2013 02 , 招待有り
  • 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, 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), 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 26
  • KSHV免疫回避分子MIRによる免疫受容体の認識機構, 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 31
  • 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,   2012 07 01
  • 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, 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 05
  • 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,   2012 03 05
  • APPの膜近傍領域の構造と膜中での会合(二量体)構造予測, 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 , 招待有り
  • 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, 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 05
  • 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, 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 05
  • 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―, 宮下尚之, 日本物理学会講演概要集,   2011 08 24
  • 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)‐‐, 宮下尚之, 杉田有治, 日本物理学会講演概要集,   2011 08 24
  • 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,   2011 08 24
  • 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,   2011 08 24
  • The development of multi-dimensional replica-exchange interface (REIN) software and the estimation of simulation time of REMD, Naoyuki Miyashita, Korea-Japan Symposium on Statistical Mechanics Approaches to Nano/Bio-Science,   2011 06 , 招待有り
  • 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, 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 27
  • 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,   2010 05 15
  • 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, 杉田有治, 宮下尚之, 今井隆志, 日本薬学会年会要旨集,   2010 03 05
  • 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, 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 01
  • 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,   2010 03 01
  • Simulation studies on the differences in the binding mechanism of LILRB1/HLA-G and LILRB2/HLA-G, 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, 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 , 招待有り
  • Dimer conformation of amyloid precursor protein fragments in the membrane, 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, Naoyuki Miyashita, John E. Straub, Yuji Sugita, Noise in complex systems, From molecular dynamics to stochastic modeling WORKSHOP 2008, Daejon, Korea,   2008 05 , 招待有り
  • 変性剤中でのプリオン蛋白質の変性の初動機構, 宮下尚之, 桑田一夫, 日本物理学会講演概要集,   2008 02 29
  • 25pPSB-47 Initial denaturation mechanism of PrPc in GdmCl., Miyashita Naoyuki, Kuwata Kazuo, Meeting abstracts of the Physical Society of Japan,   2008 02 29
  • 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, 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), Miyashita Naoyuki, Straub John E, Devarajan Thirumalai, Biophysics,   2007 11 20
  • 1P105 The function of the proton-counter transport in Ca^<2+>ATPase of sarcoplasmic reticulm, Miyashita N, Sugita Y, Ikeguchi M, Toyoshima C, Biophysics,   2004 11 10
  • 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,   2004 03 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, Miyashita Naoyuki, Yonemitsu Kenji, Meeting abstracts of the Physical Society of Japan,   2003 03 06
  • 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,   2002 08 13
  • 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,   2002 08 13
  • 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,   2002 03 01
  • 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,   2001 09 03
  • 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, 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 15
  • 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,   1999 03 15

Misc

  • 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 , http://jglobal.jst.go.jp/detail.php?from=API&JGLOBAL_ID=201502277084035050
  • 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 31 , http://jglobal.jst.go.jp/detail.php?from=API&JGLOBAL_ID=201202232207808593
  • 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,   2012 03 05 , http://ci.nii.ac.jp/naid/110009566400
  • 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 27 , http://jglobal.jst.go.jp/detail.php?from=API&JGLOBAL_ID=201102261558264681
  • 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
  • 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
  • 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
  • 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 , 10.1143/JPSJ.72.2282, http://arxiv.org/abs/cond-mat/0211487v1
    Summary: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.

Research Grants & Projects

  • 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)』, 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

社会貢献活動情報

Social Contribution

  • Dementia from a nano world, Lecturer, BOST KNDAI University,   2016 06 25  - 2016 06 25