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.