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Research

Research

We perform large-scale molecular dynamics simulations of biomolecules under cellular environments. Currently, we focus on protein stability, dynamics and functions under macromolecular crowding environment in the cytoplasm and the biological membranes.

Research Projects

  • Living cell contains 70% of water and 30% of macromolecules like proteins, nucleic acids, sugars, and so on. This environment is called as ‘macromolecular crowding environment’ and affects protein structure and stability significantly. To investigate such effect on proteins, we perform atomistic and coarse-grained molecular dynamics simulations on the macromolecular crowding systems and compare the simulation results with NMR measurements.

  • Biological membrane consists on variety of lipid molecules and membrane proteins. Recently, membrane micro-domains called as ‘lipid raft’ attract attention from researchers, because a number of essential biological processes are known to occur in lipid raft. We make molecular models of lipid raft and mixed lipid bilayers for studying membrane protein functions in the environments.

  • The aggregation and denaturation of protein in living cell appear to be linked to the Alzheimer's disease, bovine spongiform encephalopathy, and so on. We perform molecular dynamics simulations of protein aggregation and denaturation in cellular environments. This study leads to the breakthrough to understand molecular mechanism of these diseases and the information available in drug design.

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