Material

Theoretical Chemistry

Ishikita Laboratory

Material
Environment and Energy

Exploring mechanisms of proteins basedon theoretical molecular chemistry topresent a new strategy for molecular
design and bioengineering

Information

Understanding of the principles of proteinfunction on the basis of the molecular structure

Chemical Biomedicine

Proteins consist of only 20 types of amino acids, while they show large variety intheir functions, e.g., redox activity, transporter, sensor, and antibodies. To clarify
a relationship between functions and structures of proteins, we analyze molecularstructures of proteins at the atomic level and calculate physical or chemical
constants on the basis of theoretical chemistry. Certainly, functions of proteinsshould be fully explained solely by the molecular structure even if the functions
are seemingly complicated. “Just computing molecules” is not in our interest. Our
mission is to uncover new but simple principles essential to the protein sciencethrough careful analysis of the target proteins. For example, we are trying toclarify the reaction mechanisms of natural photosynthetic proteins, e.g., O2evolution, electron transfer, and proton transfer reactions. We also develop new
tools for analysis of protein function. Our challenges include:（ 1 ）T o w a r d u n d e r s t a n d i n g o f f u n c t i o n a l m e c h a n i s m s o f p r o t e i n s a n dmacromolecules for molecular design
・Electron, proton, and energy transfer reactions in photosynthesis
・Correlation between structure and functions of photoreceptor and ion
transporter・Toward more active catalytic centers: elucidation of minimum key
components that contribute to enzymatic reactions in enzymes（2）Development of new chemical theories and computational methods
・Quantum mechanics model for molecular dynamic simulation
・Theoretical prediction of acid dissociation constants( pK a ) by quantum

Barrier Free
Social Science
Laboratory forInterdiciplinary Activities
Cooperative Laboratories

chemical calculation

Professor

Hiroshi ISHIKITA
Research Area

Biophysics

Associate Professor
Research Area

Keisuke SAITO

Bio- and chemical physics

Project Associate Professor

Hiroyuki TAMURA
Assistant teacher

Tomoyasu NOJI

ColumnMy first encounter with photosynthesis researchoccurred when I went to Berlin to pursue my Ph.D.
During my undergraduate and master's studies, I
was interested in biomolecular devices. For
example, the brain of a computer (the CPU)
generates a lot of heat due to leakage current. With
this background, I wanted to create biomoleculardevices that surpassed silicon semiconductors,
which led me to pursue an engineering degree.
After being awarded a scholarship from Germany(DAAD), I was required to spend four months in
Bremen for German language studies, which
delayed the start of my research in Berlin. By thetime I arrived in Berlin, the project I had describedSocial CooperationResearch Departments

in my scholarship application was almost
completed, and instead, I was given a new topic onelectron transfer in photosynthetic reaction centerproteins. I was instantly captivated by the crystal
structure of the protein. The beauty of theCorporate SponsoredResearch Programs

symmetry in the arrangement of the pair of electrontransfer pathways and the imbalance in the
1 Electron and proton transfers in thewateroxidizing enzyme photosystem II

2 Super computer in our laboratory.

asymmetry of electron transfer activity. Solving thismystery—explaining it in terms of molecularchemistry that everyone can understand—has

Research Organization

become my life's work.

hiro@appchem.t.u-tokyo.ac.jp

https://www.protein.rcast.u-tokyo.ac.jp/
ksaito@appchem.t.u-tokyo.ac.jp

3 Exciting discussion

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