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Matsumoto, Atsushi
no journal, ,
The main goal of our study is to determine the positions of atoms in ribosomes at various phases whose 3D structures have been determined by cryo-EM, and analyze the conformational differences between them at the atomic level. We determine the atomic positions by deforming an X-ray crystal structure of ribosome computationally so that the overall shape is similar to those of the EM structures. We make use of the elastic network normal mode calculations for this purpose. This computational approach is widely used these days, and is suited for studying a large system like ribosome because it is computationally less demanding compared to the conventional techniques. By this computation, one can find conformational changes that the molecular system prefers to make, that is, low energy paths for conformational changes. We deform the X-ray crystal structure along these low energy paths and determine the atomic positions which correspond well with the EM structures.
Ishida, Hisashi; Matsumoto, Atsushi; Tsutsumi, Yu*; Yura, Kei
no journal, ,
We developed an EM density-fitting refinement method to improve the modeled 3D structure of supra-biomolecules by alleviating the steric stress of atoms while retaining the condition that the constituent molecules fit in the EM density map. Our method first uses rigid body fitting to carry out initial fitting and then uses a molecular dynamics (MD) simulation. It was found that (1) the refinement could fit the atomic structure of ribosome into the EM density maps with scores ranging from 68.5 to 83.1%, (2) the movement of the head of the 30S subunit largely contributed to the structural change of the bridge between 30S and 50S ribosome, (3) the bridges in helix 44 of 16S rRNA were well conserved throughout all the structures, (4) there were, at least, five exit tunnels with a diameter more than six angstroms, and (5) the structure of a tunnel was dynamic and its entrance was closed at the initial stage of protein synthesis.
Matsumoto, Atsushi; Takagi, Junichi*; Iwasaki, Kenji*
no journal, ,