Biophysics and Physicobiology
Online ISSN : 2189-4779
ISSN-L : 2189-4779
Current issue
Displaying 1-4 of 4 articles from this issue
Review Article (Invited)
  • Hisashi Shimamura, Hiroya Yamazaki, Shige H. Yoshimura
    Article type: Review Article (Invited)
    2024 Volume 21 Issue 2 Article ID: e210012
    Published: 2024
    Released on J-STAGE: May 03, 2024
    Advance online publication: March 28, 2024
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    Phosphorylation regulates protein function by modulating stereospecific interactions between protein-protein or enzyme-ligand. On the other hand, many bioinformatics studies have demonstrated that phosphorylation preferably occurs in intrinsically disordered regions (IDRs), which do not have any secondary and tertiary structures. Although studies have demonstrated that phosphorylation changes the phase behavior of IDRs, the mechanism, which is distinct from the “stereospecific” effect, had not been elucidated. Here, we describe how phosphorylation in IDRs regulates the protein function by modulating phase behavior. Mitotic phosphorylation in the IDRs of Ki-67 and NPM1 promotes or suppresses liquid-liquid phase separation, respectively, by altering the “charge blockiness” along the polypeptide chain. The phosphorylation-mediated regulation of liquid-liquid phase separation by enhancing or suppressing “charge blockiness,” rather than by modulating stereospecific interactions, may provide one of the general mechanisms of protein regulation by posttranslational modifications and the role of multiple phosphorylations.

Regular Article
  • Nasori Nasori, Miftakhul Firdhaus, Ulya Farahdina, Rini Khamimatul Ula
    Article type: Regular Article
    2024 Volume 21 Issue 2 Article ID: e210013
    Published: 2024
    Released on J-STAGE: May 18, 2024
    Advance online publication: April 18, 2024
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    Blood cancer is a condition in which white blood cells grow uncontrollably. Tumor treating fields (TTF) are a modality of cancer treatment that utilizes electric fields to target malignant cells. To optimize the efficacy of TTF, it is necessary to investigate the distribution of electric field through varying electrode configurations and input parameters. This allows for enhancement of electric field intensity in targeted areas while minimizing intensity in sensitive areas. Analysis of electric field distribution was conducted through simulation of brachial models with varying electrode configurations and input parameters, utilizing the COMSOL Multiphysics 5.4 software. Additionally, investigations were carried out to assess tissue dose density. The dose density value at primary target for all electrode configurations and input parameters do not exceed the threshold value (770 W/m3), whereas the electric field value at the primary target satisfied the threshold value (100 V/m) on the system that used 4 plate-shaped electrodes and arm contour-shaped electrodes with an input voltage of 20 V, and at the input voltage 15 V, only 4 arm contour-shaped electrodes that satisfied the threshold value. An increase in input voltage, electrodes addition, and electrodes adjustment to skin contour shape result in an enhancement of electric field distribution and average electric field value at primary targets.

Method and Protocol
  • Hiroyuki Iwamoto, Kazuhiro Oiwa, Kogiku Shiba, Kazuo Inaba
    Article type: Method and Protocol
    2024 Volume 21 Issue 2 Article ID: e210014
    Published: 2024
    Released on J-STAGE: May 18, 2024
    Advance online publication: April 20, 2024
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    This paper describes a method for recording X-ray diffraction patterns from a small amount of fibrous protein materials while being oriented by using a micro shear-flow cell. This cell consists of two concentrically arranged glass tubes. The inner tube is stationary, while the outer one rotates at a high speed. The gap between the two tubes is about 100 μm, into which the suspension of fibrous protein materials is injected. By using synchrotron-radiation X-ray microbeams (diameter, 10 μm), clear diffraction images from oriented protein materials can be recorded. The required volume of the sample is only about 10 μl. This method can also be combined with the laser-flash photolysis of caged compounds. Examples of application of this method to the flagella of a green alga Chlamydomonas, and sperm of a tunicate Ciona are presented.

Regular Article
  • Minoru Fukushima, Takuma Toyonaga, Yuhei O. Tahara, Daisuke Nakane, Ma ...
    Article type: Regular Article
    2024 Volume 21 Issue 2 Article ID: e210015
    Published: 2024
    Released on J-STAGE: June 19, 2024
    Advance online publication: May 28, 2024
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    Mycoplasma mobile is a parasitic bacterium that forms gliding machinery on the cell pole and glides on a solid surface in the direction of the cell pole. The gliding machinery consists of both internal and surface structures. The internal structure is divided into a bell at the front and chain structure extending from the bell. In this study, the internal structures prepared under several conditions were analyzed using negative-staining electron microscopy and electron tomography. The chains were constructed by linked motors containing two complexes similar to ATP synthase. A cylindrical spacer with a maximum diameter of 6 nm and a height of 13 nm, and anonymous linkers with a diameter of 0.9–8.3 nm and length of 14.7±6.9 nm were found between motors. The bell is bowl-shaped and features a honeycomb surface with a periodicity of 8.4 nm. The chains of the motor are connected to the rim of the bell through a wedge-shaped structure. These structures may play roles in the assembly and cooperation of gliding machinery units.

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