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