Conformational analysis of the structure of ribosome fit into electron microscopy density maps with normal mode analyses and molecular dynamics simulations

分子動力学と基準振動解析によりリボソームの電子顕微鏡像あてはめと構造変化解析

石田 恒; 松本 淳; 堤 遊*; 由良 敬

Ishida, Hisashi; Matsumoto, Atsushi; Tsutsumi, Yu*; Yura, Kei

生体超分子の電子顕微鏡像を取得することによって、いろいろな状態での構造を知ることができる。本研究では蛋白質合成生体超分子であるリボゾームの構造変化を電子顕微鏡像と計算科学の手法によって推定した。

Supra-biomolecules, which contain numerous proteins and nucleic acids, function when the constituent molecules are assembled. Therefore, it is important to determine not only the 3D structures of the constituent molecules but also the 3D structure of the supra-biomolecule. Although X-ray crystallography can determine the atomic coordinates of biomolecules, it has difficulty in handling supra-biomolecules, because crystals of huge molecules cannot be made with ease. Single particle analysis using an electron microscope (EM) has been used to observe the structure of supra-biomolecules, but the resolution of the EM image has only achieve to the atomic level in a limited situation. Therefore, several attempts have been carried out to determine the 3D structure of supra-biomolecules in atomic resolution by fitting the constituent molecules, determined by X-ray crystallography, into an EM density map. In those attempts, each constituent molecule is usually fit into the EM density map manually, and the constituent molecules may have atomic collisions at their interfaces.