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石田 恒; 松本 淳
no journal, ,
Ribosome is one of the supra-biomolecules used in the process of translating genetic information for the synthesis of polypeptides. In the course of its synthesis, two tRNA molecules move with mRNA through ribosome. This process, called translocation of tRNAs, is catalyzed by the elongation factor G (EF-G) using energy of GTP hydrolysis. We used all-atom molecular dynamics (MD) simulations to direct 70S ribosome complexed with EF-G at the post-translocational state towards the translocational and pre-translocational states by fitting 70S ribosome into cryo-EM density maps. Multistep structural changes, such as a ratchet-like motion between the small and large ribosomal subunits, and a hinge-like motion of EF-G were observed during the translocation. The free-energy landscape shows that there are semi-stable states between two stable states at the pre- and post-translational states. It was shown that a loop of nucleic acids from the large ribosomal subunit, which is located near the P- and E-sites, plays an important role in the translocation of P-tRNA and E-tRNA.
河野 秀俊
no journal, ,
The structural dynamics of two nucleosomes, one was H3 containing and other was CENP-A containing nucleosome, were characterized with molecular dynamics simulations and the findings were experimentally confirmed. The simulations showed that histone proteins of both, which is the core structure of nucleosome, are structurally stable and maintain the structure determined by X-ray crystallography, while the wrapped DNAs are highly flexible at the entry or exit region and largely deviate from the crystal structures. In particular, about 20-25 bp DNAs of entry or exit of the CENP-A containing nucleosomes showed several times of open and close conformational changes within 100ns simulations, which was not observed on the H3 containing nucleosomes. The detailed analysis clarifies that this dynamics difference is due to the difference in two basic amino acids at the 
-N helix, two Arg residues of H3 are mutated to Lys residue at the corresponding sites. The difference in ability of forming hydrogen-bond to the DNA controls the flexibility of the nucleosomal DNA at entry or exit region. This increase in flexibility was confirmed with a nuclease susceptibility assay of a nucleosome that contains H3 mutant with the two Arg residues replaced with Lys.
松本 淳; 岩崎 憲治*; 高木 淳一*
no journal, ,
We have developed a computational approach to build an atomic model from an electron microscope (EM) image of proteins. In this approach, many atomic models are built first by deforming the X-ray crystal structure of the protein using a computational technique. Then, projection images of each atomic model to many different directions are generated. Finally, they are compared to the EM image. The atomic models with the projection images similar to the EM image are regarded as the candidates for the atomic structure of the protein from which the EM image was obtained. This approach was applied to the EM images of integrin. The X-ray crystal structure of integrin was solved for the closed conformation, while many EM images were obtained for the open conformation. The difference of the two conformations is so large that it is difficult to build the atomic model for the EM conformations by deforming the X-ray crystal structure using conventional computational techniques. Thus, we have used the coarse-grained model of the X-ray crystal structure to simulate the large-scale conformational change.