KITAO Akio

J-GLOBAL         Last updated: Oct 24, 2019 at 15:43
 
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Name
KITAO Akio
URL
http://www.kitao.bio.titech.ac.jp/indexE.html
Affiliation
Tokyo Institute of Technology
Section
School of Life Science and Technology
Job title
Professor
Degree
Doctor of Science(Kyoto University), master of Science(Kyoto University)

Profile

I have been invesigating functional mechanisms of biological nano-machines. For this purpose, simulations of the behavior of biological system including nano-machines and solvent molecules in silico in atomic detail by using molecular dynamics simulation are conducted.

Research Areas

 
 

Academic & Professional Experience

 
Jul 2017
 - 
Today
Professor, School of Life Science and Technology, Tokyo Institute of Technology
 
Apr 2016
 - 
Today
Adjunct Researcher, National Institutes for Quantum and Radiological Science and Technology
 
Apr 2007
 - 
Jun 2017
Associate Professor, Institute of Molecular and Cellular Biosciences, The University of Tokyo
 
Oct 2005
 - 
Mar 2016
Research Advisor, Japan Atomic Energy Agency
 
Apr 2008
 - 
Mar 2009
Adjunct Associate Professor, Institute for Molecular Science, National Institute of Natural Sciences
 
Apr 2003
 - 
Mar 2007
Associate Professor, Institute of Molecular and Celluar Biosciences, The University of Tokyo
 
Apr 2003
 - 
Sep 2005
Research Advisor, Center for Promotion of Computational Science and Engineering, Japan Atomic Energy Research Institute
 
Feb 2002
 - 
Mar 2003
Research Scientists, Quantum Bioinformatics Group, Center for Promotion of Computational Science and Engineering, Japan Atomic Energy Research Institute
 
Apr 1993
 - 
Jan 2002
Assistant Professor, Graduate School of Science, Department of Chemistry, Kyoto University
 

Education

 
Apr 1991
 - 
Mar 1993
Department of Chemictry Doctor Course, Graduate School of Science, Kyoto University
 
Apr 1989
 - 
Mar 1991
Department of Chemictry Master Course, Graduate School of Science, Kyoto University
 
Apr 1985
 - 
Mar 1989
Mainly Physics and Chemistry, Faculty of Science, Kyoto University
 

Published Papers

 
Hanawa-Suetsugu K, Itoh Y, Ab Fatah M, Nishimura T, Takemura K, Takeshita K, Kubota S, Miyazaki N, Wan Mohamad Noor WNI, Inaba T, Nguyen NTH, Hamada-Nakahara S, Oono-Yakura K, Tachikawa M, Iwasaki K, Kohda D, Yamamoto M, Kitao A, Shimada A, Suetsugu S
Nature Communications   10(1) 4763   Dec 2019   [Refereed]
Kento Shin, Duy Phuoc Tran, Kazuhiro Takemura, Akio Kitao, Kei Terayama, Koji Tsuda
ACS Omega   4(9) 13853-13862   Aug 2019   [Refereed]
Yokochi Y, Sugiura K, Takemura K, Yoshida K, Hara S, Wakabayashi KI, Kitao A, Hisabori T
The Journal of biological chemistry      Oct 2019   [Refereed]
Onoue Y, Iwaki M, Shinobu A, Nishihara Y, Iwatsuki H, Terashima H, Kitao A, Kandori H, Homma M
Scientific Reports   9(1) 11216   Aug 2019   [Refereed]
Inoue Y, Ogawa Y, Kinoshita M, Terahara N, Shimada M, Kodera N, Ando T, Namba K, Kitao A, Imada K, Minamino T
Structure   27(6) 965-976.e6   Jun 2019   [Refereed]
Nick Matthews, Akio Kitao, Stephen Laycock, Steven Hayward
Journal of Chemical Information and Modeling   59(6) 2900-2912   Apr 2019   [Refereed]
Nakagawa H, Joti Y, Kitao A, Yamamuro O, Kataoka M
Biophysical journal   117(2) 229-238   Jul 2019   [Refereed]
Hiroaki Hata, Masayoshi Nishiyama, Akio Kitao
Biochimica et Biophysica Acta (BBA) - General Subjects      Jul 2019   [Refereed]
Duy Phuoc Tran, Akio Kitao
The Journal of Physical Chemistry B   123(11) 2469-2478   Jan 2019   [Refereed]
Ai Shinobu, Kazuhiro Takemura, Nobuyuki Matubayasi, Akio Kitao
The Journal of Chemical Physics   149(19) 194101   Dec 2018   [Refereed]
Dokainish HM, Kitao A
The journal of physical chemistry. B   122(36) 8537-8547   Sep 2018   [Refereed]
Hayward S, Kitao A
Journal of biomolecular structure & dynamics   1-38   Jul 2018   [Refereed]
Takemura K, Sato C, Kitao A
The journal of physical chemistry. B   122(29) 7191-7200   Jul 2018   [Refereed]
Yamashita S, Mizuno M, Tran DP, Dokainish H, Kitao A, Mizutani Y
The journal of physical chemistry. B   122(22) 5877-5884   Jun 2018   [Refereed]
Akio Kitao, Hiroaki Hata
Biophysical Reviews      Apr 2018   [Refereed]
Kazuhiro Takemura, Nobuyuki Matubayasi, Akio Kitao
The Journal of Chemical Physics   148(10) 105101   Mar 2018   [Refereed]
Duy Phuoc Tran, Kazuhiro Takemura, Kazuo Kuwata, Akio Kitao
Journal of Chemical Theory and Computation      Jan 2018   [Refereed]
Jacob B. Swadling, Kunihiko Ishii, Tahei Tahara, Akio Kitao
Physical Chemistry Chemical Physics   20(5) 2990   2018   [Refereed]
Kazuhiro Takemura, Kyoko Hanawa-Suetsugu, Shiro Suetsugu, Akio Kitao
Scientific Reports   7(1)    Dec 2017   [Refereed]
Jacob B. Swadling, Kunihiko Ishii, Tahei Tahara, Akio Kitao
Physical Chemistry Chemical Physics   20(5) 2990   2018   [Refereed]
Hisham M. Dokainish, Daichi Yamada, Tatsuya Iwata, Hideki Kandori, Akio Kitao
{ACS} Catalysis   7(7) 4835   Jul 2017   [Refereed]
Matthews Nick, Easdon Robert, Kitao Akio, Hayward Steven, Laycock Stephen
JOURNAL OF MOLECULAR GRAPHICS & MODELLING   78 158-167   Nov 2017   [Refereed]
Sakai T, Matsumoto Y, Ishikawa M, Sugita K, Hashimoto Y, Wakai N, Kitao A, Morishita E, Toyoshima C, Hayashi T, Akiyama T
Bioorganic & medicinal chemistry   23(2) 328-339   Jan 2015   [Refereed]
Kitao Akio, Nishihara Yasutaka
Methods in molecular biology (Clifton, N.J.)   1593 133-145   2017   [Refereed]
Harada Ryuhei, Kitao Akio
Journal of Chemical Theory and Computation   11(11) 5493-5502   2015   [Refereed]
Hayward Steven, Kitao Akio
Journal of Chemical Theory and Computation   11(8) 3895-3905   2015   [Refereed]
Maru Y, Tomita T, Deguchi A, Ieguchi K, Takita M, Tsukahara F, Takemura K, Kitao A, Gusovsky F
Endocrine, metabolic & immune disorders drug targets   15(2) 83-87   2015   [Refereed]
Otani Yuko, Watanabe Satoshi, Ohwada Tomohiko, Kitao Akio
Journal of Physical Chemistry B   121(1) 100-109   2017   [Refereed]
Kitao Akio, Takemura Kazuhiro
Current opinion in structural biology   42 50-58   2016   [Refereed]
Yamada D, Dokainish H. M, Iwata T, Yamamoto J, Ishikawa T, Todo T, Iwai S, Getzoff E. D, Kitao A, Kandori H.
Biochemistry   55(30) 4173-4183   2016   [Refereed]
Deguchi A, Tomita T, Ohto U, Takemura K, Kitao A, Akashi-Takamura S, Miyake K, Maru Y.
Oncogene   35(11) 1445-1456   2016   [Refereed]
Taguchi Junko, Kitao Akio
Biophysics and Physicobiology   13(0) 117-126   2016   [Refereed]
Dokainish Hisham M, Kitao Akio
Acs Catalysis   6(8) 5500-5507   2016   [Refereed]
Nishihara Y, Kitao A
Proceedings of the National Academy of Sciences of the United States of America   112(25) 7737-7742   Jun 2015   [Refereed]
Takahashi N, Hamada-Nakahara S, Itoh Y, Takemura K, Shimada A, Ueda Y, Kitamata M, Matsuoka R, Hanawa-Suetsugu K, Senju Y, Mori MX, Kiyonaka S, Kohda D, Kitao A, Mori Y, Suetsugu S
Nature communications   5 4994   Sep 2014   [Refereed]
Yang LW, Kitao A, Huang BC, G? N
Biophysical journal   107(6) 1415-1425   Sep 2014   [Refereed]
Wakai N, Takemura K, Morita T, Kitao A
PloS one   9(1) e85852   Jan 2014   [Refereed]
Wakai N, Takemura K, Morita T, Kitao A, PloS one, 2014, vol. 9, no. 1, pp. e85852
Yamamori Y, Kitao A
The Journal of chemical physics   139 145105   Oct 2013   [Refereed]
Harada R, Kitao A
The Journal of chemical physics   139 035103   Jul 2013   [Refereed]
Meshcheryakov VA, Kitao A, Matsunami H, Samatey FA
Acta crystallographica. Section D, Biological crystallography   69 812-820   May 2013   [Refereed]
Ishikawa T, Burri RR, Kamatari YO, Sakuraba S, Matubayasi N, Kitao A, Kuwata K
Physical chemistry chemical physics : PCCP   15(10) 3646-3654   Mar 2013   [Refereed]
Takemura K, Guo H, Sakuraba S, Matubayasi N, Kitao A
The Journal of chemical physics   137 215105   Dec 2012   [Refereed]
Takemura K, Kitao A
The journal of physical chemistry. B   116(22) 6279-6287   Jun 2012   [Refereed]
Harada R, Kitao A
Journal of Chemical Theory and Computation   8(1) 290-299   2012   [Refereed]
Nishima W, Kanamaru S, Arisaka F, Kitao A
Journal of the American Chemical Society   133(34) 13571-13576   Aug 2011   [Refereed]
Kitao A
The Journal of chemical physics   135(4) 045101   Jul 2011   [Refereed]
Harada R, Kitao A
The journal of physical chemistry. B   115(27) 8806-8812   Jul 2011   [Refereed]
Higuchi M, Fujii J, Yonetani Y, Kitao A, Go N
Journal of structural biology   173(1) 20-28   Jan 2011   [Refereed]
Harada R, Kitao A
Chemical Physics Letters   503(1-3) 145-152   2011   [Refereed]
Sakuraba S, Joti Y, Kitao A
The Journal of chemical physics   133(18) 185102   Nov 2010   [Refereed]
Hayward S, Kitao A
Biophysical journal   98(9) 1976-1985   May 2010   [Refereed]
Saijo-Hamano Y, Imada K, Minamino T, Kihara M, Shimada M, Kitao A, Namba K
Molecular microbiology   76(1) 260-268   Apr 2010   [Refereed]
Chng CP, Kitao A
Journal of molecular graphics & modelling   28(6) 548-554   Feb 2010   [Refereed]
Loeffler HH, Kitao A
Biophysical journal   97 2541-2549   Nov 2009   [Refereed]
Sakuraba S, Kitao A
Journal of computational chemistry   30(12) 1850-1858   Sep 2009   [Refereed]
Joti Y, Nakagawa H, Kataoka M, Kitao A
Biophysical journal   94 4435-4443   Jun 2008   [Refereed]
Chng CP, Kitao A
Biophysical journal   94 3858-3871   May 2008   [Refereed]
Joti Y, Nakagawa H, Kataoka M, Kitao A
The journal of physical chemistry. B   112(11) 3522-3528   Mar 2008   [Refereed]
Meinhold L, Smith JC, Kitao A, Zewail AH
Proceedings of the National Academy of Sciences of the United States of America   104(44) 17261-17265   Oct 2007   [Refereed]
Takemura K, Kitao A
The journal of physical chemistry. B   111(41) 11870-11872   Oct 2007   [Refereed]
Tokuhisa A, Joti Y, Nakagawa H, Kitao A, Kataoka M
Physical review. E, Statistical, nonlinear, and soft matter physics   75(4,Pt.1) 041912   Apr 2007   [Refereed]
Furuta T, Samatey FA, Matsunami H, Imada K, Namba K, Kitao A
Journal of structural biology   157(3) 481-490   Mar 2007   [Refereed]
Hayward S, Kitao A
Biophysical journal   91 1823-1831   Sep 2006   [Refereed]
[Protein energy landscape and dynamics studied by molecular simulations and neutron scattering].
Joti Y, Kitao A
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme   51 972-978   Jul 2006   [Refereed]
Kitao A, Wagner G
Magnetic resonance in chemistry : MRC   44 Spec No S130-42   Jul 2006   [Refereed]
Kitao A, Yonekura K, Maki-Yonekura S, Samatey FA, Imada K, Namba K, Go N
Proceedings of the National Academy of Sciences of the United States of America   103(13) 4894-4899   Mar 2006   [Refereed]
[Universal joint of biological supramolecule: mechanism of bacterial flagellar hook investigated in silico].
Kitao A, Samatey FA, Matsunami H, Imada K, Namba K
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme   50 1335-1340   Aug 2005   [Refereed]
[Structure, function and self-assembly of the bacterial flagellum].
Imada K, Samatey FA, Matsunami H, Nagashima S, Kitao A, Yonekura K, Maki-Yonekuraz S, Namba K
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme   50 1328-1334   Aug 2005   [Refereed]
Joti Y, Kitao A, Go N
Journal of the American Chemical Society   127(24) 8705-8709   Jun 2005   [Refereed]
Samatey FA, Matsunami H, Imada K, Nagashima S, Shaikh TR, Thomas DR, Chen JZ, Derosier DJ, Kitao A, Namba K
Nature   431(7012) 1062-1068   Oct 2004   [Refereed]
How can free energy component analysis explain the difference in protein stability caused by amino acid substitutions? Effect of three hydrophobic mutations at the 56th residue on the stability of human lysozyme.
Funahashi J, Sugita Y, Kitao A, Yutani K
Protein engineering   16 665-671   Sep 2003   [Refereed]
Kitao A, Wagner G
Proceedings of the National Academy of Sciences of the United States of America   97 2064-2068   Feb 2000   [Refereed]
Tama F, Miyashita O, Kitao A, Go N
European biophysics journal : EBJ   29 472-480   2000   [Refereed]
Kitao A, Go N
Current opinion in structural biology   9 164-169   Apr 1999   [Refereed]
Kitao A, Hayward S, Go N
Proteins   33 496-517   Dec 1998   [Refereed]
Computational analysis of thermal stability: effect of Ile-->Val mutations in human lysozyme.
Sugita Y, Kitao A, Go N
Folding & design   3 173-181   1998   [Refereed]
Hayward S, Kitao A, Go N
Proteins   23 177-186   Oct 1995   [Refereed]
Kitao A, Hayward S, Go N
Biophysical chemistry   52 107-114   Oct 1994   [Refereed]
Hayward S, Kitao A, Go N
Protein science : a publication of the Protein Society   3 936-943   Jun 1994   [Refereed]
Hayward S, Kitao A, Hirata F, Go N
Journal of molecular biology   234 1207-1217   Dec 1993   [Refereed]
Biomolecular Simulator, Hisashi Ishida, Yasumasa Joti, Mariko Higuchi, Takuma Kano, Akio Kitao, Nobuhiro Go
   [Refereed]
ratio of 50.5%, and a vectorization ratio of 96.9% even when 18 nodes (144 CPUs) were used. Keywords: large-scale supra-biomolecular MD simulation, PPPM method, domain decomposition method, Holliday junction 1. Introduction Molecular dynamics s...

Research Grants & Projects

 
Ministry of Education, Culture, Sports, Science and Technology: Grants-in-Aid for Scientific Research(基盤研究(B))
Project Year: 2007 - 2010    Investigator(s): Akio KITAO
To elucidate the detailed protein functional principle in broad time and space ranges, we focused on the dynamics of nano to sub-milli sec order, observed function relevant protein dynamics by molecular simulation, and studied the hyper anisotropy...
Ministry of Education, Culture, Sports, Science and Technology: Grants-in-Aid for Scientific Research(特定領域研究)
Project Year: 2004 - 2009    Investigator(s): Tomitake TSUKIHARA
We have developed X-ray crystallographic method, electron microscopic method, and their combined method to determine structures of biological macromolecular assemblies including non-crystalline substances. Theoretical method to predict structural ...
Ministry of Education, Culture, Sports, Science and Technology: Grants-in-Aid for Scientific Research(特定領域研究)
Project Year: 2004 - 2009    Investigator(s): Akio KITAO
We have developed the methods and simulation systems in which functional process of biological supramolecules is observed in silico in high resolution by using molecular simulations. We have also developed the methods to construct the structure an...
Ministry of Education, Culture, Sports, Science and Technology: Grants-in-Aid for Scientific Research(基盤研究(B))
Project Year: 2003 - 2006    Investigator(s): Akio KITAO
Bacterial flagellar filament is a macromolecular assembly consisting of single protein, flagellin. Bacterial swimming is controlled by the conformational transitions of this filament between left- and right-handed supercoils induced by the flagell...
Ministry of Education, Culture, Sports, Science and Technology: Grants-in-Aid for Scientific Research(特定領域研究(C), 特定領域研究)
Project Year: 2001 - 2004    Investigator(s): Akinori KIDERA
Database analyses of protein structures(1)Structural classification of all B-proteins: A novel structural classification of all B-proteins is presented from the viewpoint of the ring-shaped structure and the zipper-like contact pattern, based on t...
Ministry of Education, Culture, Sports, Science and Technology: Grants-in-Aid for Scientific Research(基盤研究(B))
Project Year: 1999 - 2001    Investigator(s): Akinori KIDERA
Anharmonic dynamics of a protein molecule was studied by molecular dynamics simulations of the vibrational energy transferred of myoglobin. It was found that there are two distinct schemes of the energy transfer, depending on temperature. At near ...
Ministry of Education, Culture, Sports, Science and Technology: Grants-in-Aid for Scientific Research(基盤研究(C))
Project Year: 1999 - 2001    Investigator(s): Akio KITAO
The mechanism of the CD2/CD58 complex formation was investigated by computer simulation. Our purposes of this project are 1) Investigate protein dynamics involved with the complex formation, 2) Estimate contribution from amino acid residues and en...
Ministry of Education, Culture, Sports, Science and Technology: Grants-in-Aid for Scientific Research(重点領域研究, 特定領域研究(A), 重点領域研究)
Project Year: 1995 - 1999    Investigator(s): Nobuhiro GO
The research project, "Principle of Protein Architecture," has continued its activity during FY1995-1998 for the purpose of pursuing an evolutional and/or physicochemical solution to the question "how the information of protein's three dimensional...
Ministry of Education, Culture, Sports, Science and Technology: Grants-in-Aid for Scientific Research(一般研究(C))
Project Year: 1994 - 1995    Investigator(s): Akio KITAO
Electron transfer is one of the most fundamental process in chemistry and biology. Theoretical frameworks describing non-adiabatic electron transfer process is well established through classical, semiclassical and quantum models. In all these theo...
Roles of energy landscape hierarchy and hydration structure change in molecular recognition in protein
Grant-in-Aid for Scientific Research
Project Year: 2003 - 2007
Functional analysis of bio-nano machine studied by molecular dynamics simulation
Grant-in-Aid for Scientific Research
Project Year: 2002 - 2006
Development of simulation method for functiona analysis of biomolecular supra molecules
Grant-in-Aid for Scientific Research
Project Year: 2004 - 2009
Protein Dynamics
Stability of Protein Structure
Principle of Protein Complex Formation
molecular design of proteins