11 Biomolecular Simulation

Elucidation of Structure–Function Relationship of Biological Active-Sites and New Material Design by Molecular Simulation

 Biological active-sites are regulated by protein environments and show excellent functions such as high-specific molecular recognitions and high-efficient catalysis. Our objectives are to elucidate structure–function relationship of biological active-sites by molecular simulations and to design new molecules utilizing the relationship. In particular, we focus on the Mn4CaO5 cluster in photosystem II, which efficiently oxidize water to oxygen, and heme cofactors, which show diverse biochemical functions in proteins.


[TARGET 1]  Computational determination and refinement of the 3D active-sites of biomolecules


We determine the molecular and electronic structures of unstable intermediates in the 3D active-sites of biomolecules with molecular simulations. One of the targets is to determine oxidation states and protonation patterns in the S0–S4 states of the Mn4CaO5 cluster in photosystem II.

[TARGERT 2]  Elucidation of structure–function relationship of biological active-sites by molecular simulations


We elucidate the structure–function relationship of biological active-sites by molecular simulations and find the prerequisite factors for the biological functions such as the efficient water oxidation of the Mn4CaO5 cluster in photosystem II and the variety of biochemical functions of heme in proteins.

[TARGERT 3]  Computational design of novel bio-inspired materials


Based on the obtained prerequisite factors for the biological functions, we computationally design novel bio-inspired molecules and materials.


Members

Principal Investigator

 

  Yu TAKANO

Professor, Graduate School of Information Sciences, Hiroshima City University

Research Field : computational biophysics
Comment :  Our objective is to elucidate structure–function relationship of biological active sites by molecular simulations and to design new molecules utilizing the relationship.
URL: http://www.bio.info.hiroshima-cu.ac.jp/eng/index.html

     
Co-Investigator

 

Hiroshi ISHIKITA

Professor, Research Center for Advanced Science and Technology, the University of Tokyo

Research Field :
Comment :  
URL: http://www.protein.rcast.u-tokyo.ac.jp/index_en.html

     


 

     
Collaborator


 

Yasushige YONEZAWA

Professor, Institute of Advanced Technology, Kinki University


 

Takahisa YAMATO

Associate Professor, Graduate School of Science, Nagoya University


 

Yasuteru SHIGETA

Professor, Center for Computational Sciences, University of Tsukuba


 

Katsumasa KAMIYA

Associate Professor, Center for Basic Education and Integrated Learning, Kanagawa Institute of Technology


 

Mitsuo SHOJI

Assistant Professor, Center for Computational Sciences, Unversity of Tsukuba
     

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