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

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

Proceedings of 16th International Microscopy Congress (IMC 2006), P. 242, 2006/09

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.