NAIST Graduate School of Materials Science

Supramolecular Science Laboratory

Staff & Contact
Educational StaffProf. Shun Hirota
Associate Prof. Takashi Matsuo
Assistant Prof. Satoshi Nagao, Masaru Yamanaka, Tai Hulin
TEL: +81-743-72-6110

In living organisms, a variety of biomolecules such as proteins, DNA, and sugars form unique supramolecular assemblies to maintain biofunctions. Based on chemical knowledge of the functions and structures of these bio-supramolecules at the molecular level, our laboratory focuses on elucidation of the function mechanisms and design/applications of bio-supramolecules using various spectroscopic analysis methods, protein engineering techniques, and organic syntheses.

1. New bio-supramolecules creation
We develop new protein supramolecules and polymers for functional biomaterials based on a new concept in which a protein molecule is used as a structural unit. (Fig.1)
2. Functional protein creation by protein design
We design artificial proteins with multi-active sites exhibiting antibacterial activity and ligand binding properties. (Fig. 2) These proteins are attracting attention in the biotechnology and pharmaceutical science fields.
3. Elucidation and inhibition of protein denaturalization processes
Accumulation of proteins with unusual structures in tissues causes various diseases such as Alzheimer’s disease, Parkinson’s disease, and mad cow disease (Conformation disease). We investigate denaturalization of these proteins at the molecular level and develop strategies to inhibit this denaturalization.
4. Reaction mechanism elucidation of metalloenzymes
To utilize the energy production system in nature, we elucidate the H2 production and decomposition mechanisms of a metalloenzyme, hydrogenase, using spectroscopic methods.
5. Functional analysis of physiologically active molecules for medicinal chemistry
To understand and regulate the extraordinary efficiency of bioreactions, we study action mechanisms of physiologically active small molecules from the perspective of medicinal chemistry.
6. Functional protein creation through synthetic chemistry approaches
With careful attention to precision, we design chemically attractive biocatalysts and artificial proteins with ON/OFF switchable functions, thereby creating “molecular design-based functional biomolecules”. This strategy uses the advantage of the complementarity of synthetic chemistry and biochemical approaches, in combination with genetic engineering methods. (Fig. 3)

  • Fig. 1
    Elucidated structures of cytochrome c supramolecules.
  • Fig. 2
    Creation of antibacterial protein supramolecules

Fig. 3
X-ray crystallographic structure of an artificial fluorescent protein constructed by a combination of genetic and synthetic methods

1. Y.-W. Lin, S. Nagao, M. Zhang, Y. Shomura, Y. Higuchi, S. Hirota, “Rational design of heterodimeric protein using domain swapping for myoglobin”, Angew. Chem. Int. Ed. 54 511-515 (2015).
2. A.Fujii, Y. Sekiguchi, H. Matsumura, T. Inoue, W.-S. Chung. S. Hirota, T. Matsuo, “Excimer emission properties on pyrene-labeled protein surface: correlation between emission spectra, ring stacking modes and flexibilities of pyrene probes”, Bioconjugate Chem. 26 537-548 (2015).


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