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Theme1 Five-Year Goals

(i) We will develop a coarse-grained model that consecutively connects molecular-scale (atomistic) simulations and cellular-scale simulations, and elucidate the effects of the cellular environment on protein dynamics, stability, and molecular recognition. In other words, we will recreate in the computer a life phenomenon that is otherwise realized only in an in vivo environment, like that realized by in-cell nuclear magnetic resonance (NMR), and provide necessary and valuable information to molecular biologists.
(ii) We will develop a multi-scale molecular-dynamics method that can connect different X-ray structures of membrane proteins and generate modeling of the entire transport reaction cycle through simulations. This will allow us to predict the effects of the disease-related mutants, changes in protein dynamics by inhibitors, etc. Based on the results, we plan to contribute to the realization of drug design targeted at membrane proteins.
(iii) We will perform free energy calculations for histone proteins that constitute nucleosomes, to understand and predict gene regulation by histone variants or DNA chemical modification. With the new structural and dynamic viewpoints provided by the simulation, we will contribute to epigenetic biology.

Sub Theme A

Calculations about molecular crowding and substance transport by multi-scale and multi-resolution free energy calculation methods
(Yuji Sugita・RIKEN )

 

Sub Theme B

Developments of modeling infrastructure and program code for the research of intracellular signal transduction pathway under cellular environments
(Koichi Takahashi・RIKEN )

 

Sub Theme C

Development of analysis method to simulate the change of protein stability occurred by molecular crowding
(Motonori Ota・Nagoya University)

 

Sub Theme D

Elucidation of substance transport mechanism by molecular dynamics simulation of membrane transporter
(Ryuichiro Ishitani・The University of Tokyo)

 

Sub Theme E

Computation protocol establishment of free energy profiles of changes of nucleosome position based on all-atom model
(Hidetoshi Kono・Japan Atomic Energy Agency)

 
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