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) …

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 …

Mapping mechanostable pulling geometries of a therapeutic anticalin/CTLA-4 protein complex

Z Liu, RA Moreira, A Dujmović, H Liu, B Yang… - Nano …, 2021 - ACS Publications
We used single-molecule AFM force spectroscopy (AFM-SMFS) in combination with click
chemistry to mechanically dissociate anticalin, a non-antibody protein binding scaffold, from …

Nanomechanical footprint of SARS-CoV-2 variants in complex with a potent nanobody by molecular simulations

LF Cofas-Vargas, GE Olivos-Ramirez, M Chwastyk… - Nanoscale, 2024 - pubs.rsc.org
Rational design of novel antibody therapeutics against viral infections such as coronavirus
relies on surface complementarity and high affinity for their effectiveness. Here, we explore …

An overview of several inhibitors for Alzheimer's disease: characterization and failure

S Boopathi, AB Poma, R Garduño-Juárez - International Journal of …, 2021 - mdpi.com
Amyloid beta (Aβ) oligomers are the most neurotoxic aggregates causing neuronal death
and cognitive damage. A detailed elucidation of the aggregation pathways from oligomers to …

A brief history of amyloid aggregation simulations

H Fatafta, M Khaled, B Kav, OO Olubiyi… - Wiley Interdisciplinary …, 2024 - Wiley Online Library
Amyloid proteins are characterized by their tendency to aggregate into amyloid fibrils, which
are often associated with devastating diseases. Aggregation pathways typically involve …

The G\= oMartini approach: Revisiting the concept of contact maps and the modelling of protein complexes

LF Cofas-Vargas, RA Moreira, S Poblete… - arXiv preprint arXiv …, 2023 - arxiv.org
We present a review of a series of contact maps for the determination of native interactions
in proteins and nucleic acids based on a distance-threshold. Such contact maps are mostly …

Comprehending the Efficacy of Whitlock's Caffeine-Pincered Molecular Tweezer on β-Amyloid Aggregation

M Devi, S Paul - ACS Chemical Neuroscience, 2024 - ACS Publications
Alzheimer's disease (AD) stands as one of the most prevalent neurodegenerative
conditions, leading to cognitive impairment, with no cure and preventive measures …

Simulations of cross-amyloid aggregation of amyloid-β and islet amyloid polypeptide fragments

GE Kawecki, KM King, NA Cramer, DR Bevan… - Biophysical …, 2022 - cell.com
Amyloid-β (Aβ) and islet amyloid polypeptide (IAPP) are small peptides, classified as
amyloids, that have the potential to self-assemble and form cytotoxic species, such as small …

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 …