Theoretical Chemistry Ishikita Laboratory
Understanding of the principles of protein function on the basis of the molecular structure
Proteins consist of only 20 types of amino acids, while they show large variety in their functions, e.g., redox activity, transporter, sensor, and antibodies. To clarify a relationship between functions and structures of proteins, we analyze molecular structures of proteins at the atomic level and calculate physical or chemical constants on the basis of theoretical chemistry.
Certainly, functions of proteins should 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 science through careful analysis of the target proteins. For example, we are trying to clarify the reaction mechanisms of natural photosynthetic proteins, e.g., O2- evolution, electron transfer, and proton transfer reactions. We also develop new tools for analysis of protein function.
Our challenges include:
(1)Toward understanding of functional mechanisms of proteins and macromolecules 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 (pKa) by quantum chemical calculation
Specialized field：Biophysics, Theoretical chemistry, Protein, Photosynthesis, Electron transfer, Proton transfer
Specialized field：Bio-and chemical physics, Photosynthesis, Electron/proton/Excitation-energy transfer