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  1. Article ; Online: Free energy profile for unwrapping outer superhelical turn of CENP-A nucleosome

    Hidetoshi Kono / Shun Sakuraba / Hisashi Ishida

    Biophysics and Physicobiology, Vol

    2019  Volume 16

    Abstract: Eukaryotic genome is packaged in a nucleus in the form of chromatin. The fundamental structural unit of the chromatin is the protein-DNA complex, nucleosome, where DNA of about 150 bp is wrapped around a histone core almost twice. In cellular processes ... ...

    Abstract Eukaryotic genome is packaged in a nucleus in the form of chromatin. The fundamental structural unit of the chromatin is the protein-DNA complex, nucleosome, where DNA of about 150 bp is wrapped around a histone core almost twice. In cellular processes such as gene expression, DNA repair and duplication, the nucleosomal DNA has to be unwrapped. Histone proteins have their variants, indicating there are a variety of constitutions of nucleosomes. These different constitutions are observed in different cellular processes. To investigate differences among nucleosomes, we calculated free energy profiles for unwrapping the outer superhelical turn of CENP-A nucleosome and compared them with those of the canonical nucleosome. The free energy profiles for CENP-A nucleosome suggest that CENP-A nucleosome is the most stable when 16 to 22 bps are unwrapped in total whereas the canonical nucleosome is the most stable when it is fully wrapped. This indicates that the flexible conformation of CENP-A nucleosome is ready to provide binding sites for the structural integrity of the centromere.
    Keywords cenp-a ; nucleosome ; unwrapping ; free energy ; molecular dynamics ; Biology (General) ; QH301-705.5 ; Physiology ; QP1-981 ; Physics ; QC1-999
    Subject code 612
    Language English
    Publishing date 2019-11-01T00:00:00Z
    Publisher The Biophysical Society of Japan
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Correction

    Hidetoshi Kono / Shun Sakuraba / Hisashi Ishida

    PLoS Computational Biology, Vol 15, Iss 10, p e

    Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA.

    2019  Volume 1007439

    Abstract: This corrects the article DOI:10.1371/journal.pcbi.1006024.]. ...

    Abstract [This corrects the article DOI:10.1371/journal.pcbi.1006024.].
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2019-10-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

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  3. Article ; Online: Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA.

    Hidetoshi Kono / Shun Sakuraba / Hisashi Ishida

    PLoS Computational Biology, Vol 14, Iss 3, p e

    2018  Volume 1006024

    Abstract: The eukaryotic genome is packaged into a nucleus in the form of chromatin. The fundamental structural unit of chromatin is a protein-DNA complex, the nucleosome, where 146 or 147 base pairs of DNA wrap 1.75 times around a histone core. To function in ... ...

    Abstract The eukaryotic genome is packaged into a nucleus in the form of chromatin. The fundamental structural unit of chromatin is a protein-DNA complex, the nucleosome, where 146 or 147 base pairs of DNA wrap 1.75 times around a histone core. To function in cellular processes, however, nucleosomal DNA must be unwrapped. Although this unwrapping has been experimentally investigated, details of the process at an atomic level are not yet well understood. Here, we used molecular dynamics simulation with an enhanced sampling method to calculate the free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA. A free energy change of about 11.5 kcal/mol for the unwrapping agrees well with values obtained in single molecule experiments. This simulation revealed a variety of conformational states, indicating there are many potential paths to outer superhelicdal turn unwrapping, but the dominant path is likely asymmetric. At one end of the DNA, the first five bps unwrap, after which a second five bps unwrap at the same end with no increase in free energy. The unwrapping then starts at the other end of the DNA, where 10 bps are unwrapped. During further unwrapping of 15 bps, the unwrapping advances at one of the ends, after which the other end of the DNA unwraps to complete the unwrapping of the outer superhelical turn. These results provide insight into the construction, disruption, and repositioning of nucleosomes, which are continuously ongoing during cellular processes.
    Keywords Biology (General) ; QH301-705.5
    Subject code 612
    Language English
    Publishing date 2018-03-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Free-energy landscape of reverse tRNA translocation through the ribosome analyzed by electron microscopy density maps and molecular dynamics simulations.

    Hisashi Ishida / Atsushi Matsumoto

    PLoS ONE, Vol 9, Iss 7, p e

    2014  Volume 101951

    Abstract: To understand the mechanism of reverse tRNA translocation in the ribosome, all-atom molecular dynamics simulations of the ribosome-tRNAs-mRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the ... ...

    Abstract To understand the mechanism of reverse tRNA translocation in the ribosome, all-atom molecular dynamics simulations of the ribosome-tRNAs-mRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-EM density maps. Between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. Multistep structural changes, such as a ratchet-like motion and rotation of the head of the small subunit were observed. The free-energy landscape showed that there were two main free-energy barriers: one between the post-translocational and intermediate states, and the other between the pre-translocational and intermediate states. The former corresponded to a clockwise rotation, which was coupled to the movement of P-tRNA over the P/E-gate made of G1338, A1339 and A790 in the small subunit. The latter corresponded to an anticlockwise rotation of the head, which was coupled to the location of the two tRNAs in the hybrid state. This indicates that the coupled motion of the head rotation and tRNA translocation plays an important role in opening and closing of the P/E-gate during the ratchet-like movement in the ribosome. Conformational change of EF-G was interpreted to be the result of the combination of the external motion by L12 around an axis passing near the sarcin-ricin loop, and internal hinge-bending motion. These motions contributed to the movement of domain IV of EF-G to maintain its interaction with A/P-tRNA.
    Keywords Medicine ; R ; Science ; Q
    Subject code 541
    Language English
    Publishing date 2014-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Clinical factors associated with the therapeutic efficacy of atezolizumab plus bevacizumab in patients with unresectable hepatocellular carcinoma

    Machiko Kai / Hayato Hikita / Maesaka Kazuki / Yuki Tahata / Kazuma Shinkai / Akira Doi / Kazuyoshi Ohkawa / Masanori Miyazaki / Hisashi Ishida / Kengo Matsumoto / Yasutoshi Nozaki / Takayuki Yakushijin / Ryotaro Sakamori / Akira Kaneko / Sadaharu Iio / Takatoshi Nawa / Naruyasu Kakita / Naoki Morishita / Naoki Hiramatsu /
    Takeo Usui / Kazuho Imanaka / Yoshinori Doi / Mitsuru Sakakibara / Yuichi Yoshida / Tsugiko Oze / Takahiro Kodama / Tomohide Tatsumi / Tetsuo Takehara

    PLoS ONE, Vol 19, Iss

    A multicenter prospective observational study

    2024  Volume 1

    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

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