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Affiliation |
Faculty of Science Department of Chemistry and Biological Science |
ITOH Satoru G.
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Research Areas 【 display / non-display 】
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Natural Science / Biophysics, chemical physics and soft matter physics
From Graduate School 【 display / non-display 】
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The Graduate University for Advanced Studies Graduate School, Division of Physics Doctor's Course Completed
- 2005.03
Papers 【 display / non-display 】
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Single-Molecule Kinetic Observation of Antibody Interactions with Growing Amyloid β Fibrils
Maho Yagi-Utsumi, Yui Kanaoka, Shogo Miyajima, Satoru G. Itoh, Katsuhiko Yanagisawa, Hisashi Okumura, Takayuki Uchihashi, Koichi Kato
Journal of the american chemical society 2024.10
Publishing type：Research paper (scientific journal)
DOI： 10.1021/jacs.4c08841
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Daiki Fukuhara, Satoru G. Itoh, Hisashi Okumura
Biophysics and Physicobiology 20 ( 4 ) n/a - n/a 2023.12
Publishing type：Research paper (scientific journal) Publisher：Biophysical Society of Japan
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Dissociation process of polyalanine aggregates by free electron laser irradiation
Hisashi Okumura, Satoru G. Itoh, Heishun Zen, Kazuhiro Nakamura
PLOS ONE 18 ( 9 ) e0291093 - e0291093 2023.09
Publishing type：Research paper (scientific journal) Publisher：Public Library of Science (PLoS)
Polyalanine (polyA) disease-causative proteins with an expansion of alanine repeats can be aggregated. Although curative treatments for polyA diseases have not been explored, the dissociation of polyA aggregates likely reduces the cytotoxicity of polyA. Mid-infrared free electron laser (FEL) successfully dissociated multiple aggregates. However, whether the FEL dissociates polyA aggregates like other aggregates has not been tested. Here, we show that FEL at 6.1 μm experimentally weakened the extent of aggregation of a peptide with 13 alanine repeats (13A), and the irradiated 13A exerted lesser cytotoxicity to neuron-like cells than non-irradiated 13A. Then, we applied molecular dynamics (MD) simulation to follow the dissociation process by FEL. We successfully observed how the intermolecular β-sheet of polyA aggregates was dissociated and separated into monomers with helix structures upon FEL irradiation. After the dissociation by FEL, water molecules inhibited the reformation of polyA aggregates. We recently verified the same dissociation process using FEL-treated amyloid-β aggregates. Thus, a common mechanism underlies the dissociation of different protein aggregates that cause different diseases, polyA disease and Alzheimer’s disease. However, MD simulation indicated that polyA aggregates are less easily dissociated than amyloid-β aggregates and require longer laser irradiation due to hydrophobic alanine repeats.
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Maho Yagi-Utsumi, Satoru G. Itoh, Hisashi Okumura, Katsuhiko Yanagisawa, Koichi Kato, Katsuyuki Nishimura
ACS Chemical Neuroscience 14 ( 15 ) 2648 - 2657 2023.07
Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS)
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Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency
Daiki Fukuhara, Masataka Yamauchi, Satoru G. Itoh, Hisashi Okumura
JOURNAL OF COMPUTATIONAL CHEMISTRY 44 ( 4 ) 534 - 545 2023.02
Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1002/jcc.27020
Scientific Research Funds Acquisition Results 【 display / non-display 】
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Aggregation process of amyloid-beta peptides on a membrane on a lipid membrane studied by computer simulation
Grant number：21K06040 2021.04 - 2024.03
Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)
Grant amount：\2730000 （ Direct Cost: \2100000 、 Indirect Cost：\630000 ）
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Oligomer formation of amyloid-beta studied by new constant pH simulations
Grant number：16K18531 2016.04 - 2019.03
Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B) Grant-in-Aid for Young Scientists (B)
Itoh Satoru
Grant amount：\2990000 （ Direct Cost: \2300000 、 Indirect Cost：\690000 ）
The oligomer formation process of Abeta(29-42), which is a fragment of the amyloid beta (Abeta) peptide, was studied by Coulomb replica-permutation molecular dynamics simulations. It was found that an oligomer increased in size by addition of a monomer to the oligomer sequentially.
We also performed Coulomb replica-permutation molecular dynamics simulations to clarify the dimer formation process of the full-length Abeta peptides. As a result, it was found that the intramolecular beta-sheet structure accelerated the formation of an intermolecular beta-sheet structure. -
Oligomerization of amyloid beta-peptides studies by computer simulations
Grant number：24740296 2012.04 - 2015.03
Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B) Grant-in-Aid for Young Scientists (B)
ITOH Satoru
Grant amount：\2340000 （ Direct Cost: \1800000 、 Indirect Cost：\540000 ）
I had developed new simulation methods, the replica-permutation method and the Hamiltonian replica-permutation method. By using these methods, efficient conformational sampling for biomolecules can be realized in comparison with existing simulation methods. I had studied the oligomerization process of amyloid-beta peptides by these new methods. As a result, it was shown that beta-hairpin structures were increased when the amyloid-beta peptides came close. When the amyloid-beta peptides got close sufficiently, intermolecular beta-sheet structures as seen in amyloid fibrils were readily created in the presence of intramolecular beta-sheet structures.