Molecular dynamics simulation studies on the aggregation of amyloid-β peptides and their disaggregation by ultrasonic wave and infrared laser irradiation

H Okumura, SG Itoh - Molecules, 2022 - mdpi.com
Alzheimer's disease is understood to be caused by amyloid fibrils and oligomers formed by
aggregated amyloid-β (Aβ) peptides. This review article presents molecular dynamics (MD) …

SEVI inhibits Aβ amyloid aggregation by capping the β-sheet elongation edges

Y Wang, J Xu, F Huang, J Yan, X Fan… - Journal of Chemical …, 2023 - ACS Publications
Inhibiting the aggregation of amyloid peptides with endogenous peptides has broad interest
due to their intrinsically high biocompatibility and low immunogenicity. Here, we investigated …

Key residue for aggregation of amyloid-β peptides

SG Itoh, M Yagi-Utsumi, K Kato… - ACS Chemical …, 2022 - ACS Publications
It is known that oligomers of amyloid-β (Aβ) peptide are associated with Alzheimer's disease.
Aβ has two isoforms: Aβ40 and Aβ42. Although the difference between Aβ40 and Aβ42 is …

Perspective for Molecular Dynamics Simulation Studies of Amyloid-β Aggregates

H Okumura - The Journal of Physical Chemistry B, 2023 - ACS Publications
The cause of Alzheimer's disease is related to aggregates such as oligomers and amyloid
fibrils consisting of amyloid-β (Aβ) peptides. Molecular dynamics (MD) simulation studies …

Inhibition Effect and Molecular Mechanisms of Quercetin on the Aβ42 Dimer: A Molecular Dynamics Simulation Study

M Fang, X Wang, K Su, X Jia, P Guan, X Hu - ACS omega, 2023 - ACS Publications
Amyloid-β (Aβ) dimer as the smallest oligomer has recently been drawing attention due to its
neurotoxicity, transient nature, and heterogeneity. The inhibition of Aβ dimer's aggregation is …

Replica permutation with solute tempering for molecular dynamics simulation and its application to the dimerization of amyloid-β fragments

D Fukuhara, SG Itoh, H Okumura - The Journal of Chemical Physics, 2022 - pubs.aip.org
We propose the replica permutation with solute tempering (RPST) by combining the replica-
permutation method (RPM) and the replica exchange with solute tempering (REST) …

Dissociation process of polyalanine aggregates by free electron laser irradiation

H Okumura, SG Itoh, H Zen, K Nakamura - PLoS One, 2023 - journals.plos.org
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 …

[HTML][HTML] Application study of infrared free-electron lasers towards the development of amyloidosis therapy

M Jindo, K Nakamura, H Okumura… - Journal of Synchrotron …, 2022 - scripts.iucr.org
Amyloidosis is known to be caused by the deposition of amyloid fibrils into various biological
tissues; effective treatments for the disease are little established today. An infrared free …

Can local heating and molecular crowders disintegrate amyloid aggregates?

N Kumar, P Khatua, SK Sinha - Chemical Science, 2024 - pubs.rsc.org
The present study employs a blend of molecular dynamics simulations and a theoretical
model to explore the potential disintegration mechanism of a matured Aβ octamer, aiming to …

Nowhere to run: oligo (p-phenylene vinylene) kills oral intracellular bacteria photodynamically

L Yuan, X Fu, W Yu, H Wei, F dong, L Zhang… - NPG Asia …, 2023 - nature.com
Bacterial infections pose a severe threat to human health due to the exacerbation of
antibiotic resistance and intracellular bacterial infections. Research suggests that oligo (p …