リボソーム及びリボソームトンネルを通る新生ポリペプチド鎖の分子動力学シミュレーション

Molecular dynamics simulation of the 70S ribosome and nascent polypeptide passing through the exit tunnel

石田 恒; 由良 敬

Ishida, Hisashi; Yura, Kei

Ribosome is one of the supra-biomolecules used in the process of translating genetic information to polypeptides. In order to understand the dynamic properties of the ribosome and the nascent polypeptide, molecular dynamics simulations of the 70S ribosome were performed. A principal component analysis (PCA) on dynamics trajectories revealed collective motions of the 70S ribosome and a low frequency mode showed a so-called ratchet-like motion of the 30S and 50S subunits. We further performed steered molecular dynamics simulation and pulled the nascent polypeptide during the simulation to observe the interactions between the nascent polypeptide and a gate of the tunnel formed by the L4 and L22 proteins. This gate has been considered flexible and to play an active role in the elongation of the nascent polypeptides. Our simulation, however, suggested that the gate was not as flexible as was generally thought.