Structural analysis of ribosome based on the elastic network normal mode analysis and fitting technique

Matsumoto, Atsushi; Ishida, Hisashi

no journal, , 

Recently, many three-dimensional structures of ribosome at various phases during the process of translating RNA to protein have been determined by cryo-electron microscopy (cryo-EM) and reconstruction techniques. In this study, we compared the 3D cryo-EM structures of ribosome by using normal mode analysis of the elastic network model and fitting technique. The atomic structure of ribosome solved by X-ray crystallography was deformed by the normal mode analysis and a library of the deformed atomic structures was built. The library was then searched to find the atomic structure which fit well into each EM structure of ribosome. For this search, we used the fitting technique, in which the entire atomic structure is translated and rotated as a rigid body so that it overlaps a 3D EM structure at the maximum ratio. We, then, compared the atomic structures thus obtained and found that the ribosome prefers ratchet-like motions.

Infrared spectroscopic studies on a protein in a reverse micelle

Murakami, Hiroshi; Nishi, Takaki; Toyota, Yuji

no journal, , 

no abstracts in English

Molecular dynamics simulation of clustered DNA damage site including single strand brake

Higuchi, Mariko; Pinak, M.; Saito, Kimiaki

no journal, , 

Ionizing radiation leads to clustered DNA damage sites. These sites are repaired with less efficiency than single lesions. So far the detail mechanism of repair of multiple lesions is not known. A lesion which locates within a few base pairs opposite to a 8oxo-G tends to inhibit excision of the 8oxo-G by repair enzyme MutM. The strength of inhibition effect is difference according to a kind of lesion. The inhibition effect of - single strand break (SSB) is stronger than that of SSB and abasic (AP) site. In this study, we present the results of molecular dynamics (MD) simulation, by comparing (1) - SSB, (2) SSB and (3) the AP site in cluster damaged DNA which is containing 8-oxoG. We discuss with the relation between the structural change of cluster damaged DNA and the inhibition effect.

Effects of TnT mutations causing hypertrophic cardiomyopathy on the physiological functions of single myofibrils

Matsumoto, Fumiko; Piroddi, N.*; Belus, A.*; Scellini, B.*; Maeda, Kayo*; Tesi, C.*; Poggesi, C.*; Maeda, Yuichiro*; Fujiwara, Satoru

no journal, , 

We showed that two Hypertrophic Cardiomyopathy -associated mutations of TnT, E244D and K247R, increase the maximum ATPase activity without any change in Ca ion sensitivity in BSJ 2007. It is, however, still not clear if the mutations have direct effects on the muscle. We thus examined the maximal isometric tension and kinetics of Tn-exchanged myofibrils by use single myofibril. The results indicate that the effects of the mutations on the physiological function of the myofibrils are directly coupled with the effects on the ATPase activity. And the mutant TnT exchanged myofibrils had similar kinetics as the wild type.

Theoretical approach for solving 3D structures of biomolecules with single-molecule X-ray diffraction patterns

Tokuhisa, Atsushi; Taka, Junichiro; Moribayashi, Kengo; Otobe, Tomohito; Kai, Takeshi; Nakamura, Tatsufumi; Fukuda, Yuji; Kono, Hidetoshi; Go, Nobuhiro

no journal, ,