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Dynamics of biological molecules are essential for their functions. Biological molecules interact with other molecules (small chemical or biological molecules) and undergo conformational transitions through out their functional processes. Thus characterization of these motions are important to understand the mechanisms, however biological molecules are small in scale and direct observation of their motions is still difficult in the current experimental techniques.
Casein Kinase Dynamics
Molecular dynamics simulation is a powerful technique to obtain additional insights by providing atomistic level details of molecular motions. Molecular dynamics simulation is a computational technique to simulate the dynamics of biological molecules. In this approach, the potential energy functions that represent physicochemical properties of proteins and nucleotides are defined and equation of motion is numerically solved using high performance computers. Being computer simulations, the whole descriptions of atomic motions can be examined.
We perform molecular dynamics simulations of biological molecules to examine a variety of functions. We can study their interactions with other molecules, for example, other proteins or drug molecules. We also study conformational transitions following such interactions. Observations from simulations are examined carefully to discover new insights that have not been accessible from experimental studies. Recent studies include small heat shock proteins and organic cation transporter proteins.
Network analysis of the conformational states of Heat Shock Proteins,
More recently in collaboration with Dr. Hirota from ITbM, we have been studying proteins involved in the maintanance of circadian rythm such as protein kinases and cryptochrome proteins. We have been able to highligth the importance of dynamics in the function of those biomolecules as well as elucitading via protein ligand docking interactions between the proteins and some newly developed small molecules.
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