Search Results - "Itoh, G."

Dissociation process of polyalanine aggregates by free electron laser irradiation by Okumura, Hisashi, Itoh, Satoru G, Zen, Heishun, Nakamura, Kazuhiro

“…Polyalanine (polyA) disease-causative proteins with an expansion of alanine repeats can be aggregated. Although curative treatments for polyA diseases have not…”
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Amyloid Fibril Disruption by Ultrasonic Cavitation: Nonequilibrium Molecular Dynamics Simulations by Okumura, Hisashi, Itoh, Satoru G

“…We describe the disruption of amyloid fibrils of Alzheimer’s amyloid-β peptides by ultrasonic cavitation. For this purpose, we performed nonequilibrium…”
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Molecular Dynamics Simulation Studies on the Aggregation of Amyloid-β Peptides and Their Disaggregation by Ultrasonic Wave and Infrared Laser Irradiation by Okumura, Hisashi, Itoh, Satoru G

“…Alzheimer's disease is understood to be caused by amyloid fibrils and oligomers formed by aggregated amyloid-β (Aβ) peptides. This review article presents…”
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Promotion and Inhibition of Amyloid-β Peptide Aggregation: Molecular Dynamics Studies by Itoh, Satoru G, Okumura, Hisashi

“…Aggregates of amyloid-β (Aβ) peptides are known to be related to Alzheimer's disease. Their aggregation is enhanced at hydrophilic-hydrophobic interfaces, such…”
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Role of Water Molecules and Helix Structure Stabilization in the Laser-Induced Disruption of Amyloid Fibrils Observed by Nonequilibrium Molecular Dynamics Simulations by Okumura, Hisashi, Itoh, Satoru G, Nakamura, Kazuhiro, Kawasaki, Takayasu

“…Water plays a crucial role in the formation and destruction of biomolecular structures. The mechanism for destroying biomolecular structures was thought to be…”
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All-Atom Molecular Dynamics Simulation Methods for the Aggregation of Protein and Peptides: Replica Exchange/Permutation and Nonequilibrium Simulations by Itoh, Satoru G, Okumura, Hisashi

“…Protein aggregates are associated with more than 40 serious human diseases. To understand the formation mechanism of protein aggregates at atomic level,…”
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Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency by Fukuhara, Daiki, Yamauchi, Masataka, Itoh, Satoru G., Okumura, Hisashi

“…In the replica‐permutation method, an advanced version of the replica‐exchange method, all combinations of replicas and parameters are considered for parameter…”
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State-of-the-Art Molecular Dynamics Simulation Studies of RNA-Dependent RNA Polymerase of SARS-CoV-2 by Tanimoto, Shoichi, Itoh, Satoru G., Okumura, Hisashi

“…Molecular dynamics (MD) simulations are powerful theoretical methods that can reveal biomolecular properties, such as structure, fluctuations, and ligand…”
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Tardigrade Secretory-Abundant Heat-Soluble Protein Varies Entrance Propensity Depending on the Amino-Acid Sequence by Miyazawa, Kazuhisa, Itoh, Satoru G, Yoshida, Yuki, Arakawa, Kazuharu, Okumura, Hisashi

“…Secretory-abundant heat-soluble (SAHS) proteins, which constitute a protein family unique to tardigrades, are thought to be essential for anhydrobiosis. Our…”
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Cancer-associated fibroblasts induce cancer cell apoptosis that regulates invasion mode of tumours by Itoh, G, Chida, S, Yanagihara, K, Yashiro, M, Aiba, N, Tanaka, M

“…In the process of cancer spreading, different modes of invasion exist. One is expansive invasion, in which a group of cancer cells gradually expands along with…”
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pH replica-exchange method based on discrete protonation states by Itoh, Satoru G., Damjanović, Ana, Brooks, Bernard R.

“…We propose a new algorithm for obtaining proton titration curves of ionizable residues. The algorithm is a pH replica‐exchange method (PHREM), which is based…”
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Structural basis of TRPA1 inhibition by HC-030031 utilizing species-specific differences by Gupta, Rupali, Saito, Shigeru, Mori, Yoshiharu, Itoh, Satoru G., Okumura, Hisashi, Tominaga, Makoto

“…Pain is a harmful sensation that arises from noxious stimuli. Transient receptor potential ankyrin 1 (TRPA1) is one target for studying pain mechanisms. TRPA1…”
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Energetics and kinetics of substrate analog-coupled staphylococcal nuclease folding revealed by a statistical mechanical approach by Mizukami, Takuya, Furuzawa, Shunta, Itoh, Satoru G., Segawa, Saho, Ikura, Teikichi, Ihara, Kunio, Okumura, Hisashi, Roder, Heinrich, Maki, Kosuke

“…Protein conformational changes associated with ligand binding, especially those involving intrinsically disordered proteins, are mediated by tightly coupled…”
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Coulomb replica-exchange method: Handling electrostatic attractive and repulsive forces for biomolecules by Itoh, Satoru G., Okumura, Hisashi

“…We propose a new type of the Hamiltonian replica‐exchange method (REM) for molecular dynamics (MD) and Monte Carlo simulations, which we refer to as the…”
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Critical contributions of pre-S1 shoulder and distal TRP box in DAG-activated TRPC6 channel by PIP2 regulation by Mori, Masayuki X., Okada, Ryo, Sakaguchi, Reiko, Hase, Hideharu, Imai, Yuko, Polat, Onur K., Itoh, Satoru G., Okumura, Hisashi, Mori, Yasuo, Okamura, Yasushi, Inoue, Ryuji

“…Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P 2 or PIP 2 ) regulates the activities of numerous membrane proteins, including diacylglycerol(DAG)-activated…”
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Inhibition of amyloid-β(16–22) aggregation by polyphenols using replica permutation with solute tempering molecular dynamics simulation by Fukuhara, Daiki, Itoh, Satoru G., Okumura, Hisashi

“…Aggregates of amyloid-β (Aβ) peptides are thought to cause Alzheimer’s disease. Polyphenolic compounds are known to inhibit Aβ aggregation. We applied replica…”
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Molecular dynamics simulations of amyloid-β peptides in heterogeneous environments by Tachi, Yuhei, Itoh, Satoru G., Okumura, Hisashi

“…Alzheimer’s disease is thought to be caused by the aggregation of amyloid-β (Aβ) peptides. Their aggregation is accelerated at hydrophilic/hydrophobic…”
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Structural basis for promiscuous action of monoterpenes on TRP channels by Nguyen, Thi Hong Dung, Itoh, Satoru G., Okumura, Hisashi, Tominaga, Makoto

“…Monoterpenes are major constituents of plant-derived essential oils and have long been widely used for therapeutic and cosmetic applications. The monoterpenes…”
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Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules by Itoh, Satoru G, Okumura, Hisashi, Okamoto, Yuko

“…We present a new type of the Hamiltonian replica-exchange method, where the van der Waals radius parameter and not the temperature is exchanged. By decreasing…”
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Microscopic 3-dimensional mapping of hydrogen bubbles in polycrystalline Al by elastic recoil detection analysis under transmission geometry by Yamazaki, A., Sasa, K., Tomita, S., Ishii, S., Naramoto, H., Sataka, M., Kudo, H., Itoh, G., Ohkubo, M.

“…We have measured microscopic 3-dimensional distribution of plasma-charged hydrogen in polycrystalline Al. The measurements have been carried out…”
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