Flexible dynamics of proteins and their functions

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Trough the 3-year project, we have developed new methods of computation of protein dynamics and investigated processes of protein functioning.(1) A coarse-grained method to simulate protein dynamics was newly developed and applied to the force-generation process of actomyosin system. Cooperative effects of the lever-arm swinging motion and the sliding motion of myosin head were found.(2) Folding process of proteins were investigated by using GO-like models. Complexity in the folding process of nearly symmetrical proteins was revealed by showing the co-existence of multiple pathways and the mechanism of selection of specific routes among them.(3) A novel concept of functional funnel was introduced by analyzing the functioning process of a photo-sensing protein.(4) 3-D structures of proteins were predicted from sequences by developing a new method to simulate the folding process. We attended the international contest for structure prediction, CASP7, and acquired fairly good scores in a category of new-fold prediction.(5) Sequence selection was simulated by computer. We found that by selecting sequences which have desired local configuration at the active-site, random sequences can evolve into the foldable protein-like sequences.(6) Hydrophobic hydration around the nano-meter size solutes were investigated by molecular dynamics simulation and the topology-sensitive hydration and hydrophobic interaction were found.