Molecular dynamics studies of α-helix stability in fibril-forming peptides

E Nordling, Y Kallberg, J Johansson… - Journal of Computer …, 2008 - Springer
Diseases associated with protein fibril-formation, such as the prion diseases and
Alzheimer's disease, are gaining increased attention due to their medical importance and …

Multiple β‐sheet molecular dynamics of amyloid formation from two ABl‐SH3 domain peptides

D Lapidus, V Duka, V Stonkus, C Czaplewski… - Peptide …, 2012 - Wiley Online Library
Molecular dynamics simulations in explicit water were carried out for two stacks, each
composed of six 10‐strand antiparallel β‐sheets for two peptides corresponding to the …

The effect of sodium dodecyl sulfate concentration on the aggregation behavior of Aβ (1–42) peptide: Molecular dynamics simulation approach

A Ahmadzade, MR Bozorgmehr, E Parvaee - Journal of Molecular Liquids, 2020 - Elsevier
Abstract Beta-amyloid (1–42) is the most effective peptide in the formation of inter-synaptic
aggregate structures. These complex structures lead to disruption of the neural network and …

Modeling the α-helix to β-hairpin transition mechanism and the formation of oligomeric aggregates of the fibrillogenic peptide Aβ (12–28): insights from all-atom …

F Simona, G Tiana, RA Broglia, G Colombo - Journal of Molecular Graphics …, 2004 - Elsevier
In this paper, all-atom molecular dynamics simulations in explicit solvent are used to
investigate the structural and dynamical determinants of the α-helical to β-hairpin …

Revealing hidden helix propensity in Aβ peptides by molecular dynamics simulations

C Lockhart, DK Klimov - The Journal of Physical Chemistry B, 2013 - ACS Publications
Using all-atom explicit solvent model and exhaustive replica exchange molecular dynamics
simulations we studied the conformational ensembles of several amino-truncated Aβ …

Interpeptide interactions induce helix to strand structural transition in Aβ peptides

T Takeda, DK Klimov - Proteins: Structure, Function, and …, 2009 - Wiley Online Library
Replica exchange molecular dynamics and all‐atom implicit solvent model are used to
compute the structural propensities in Aβ monomers, dimers, and Aβ peptides bound to the …

The effects of aspartic acid‐bond isomerization on in vitro properties of the amyloid β‐peptide as modeled with N‐terminal decapeptide fragments

GI SZENDREI, KV PRAMMER… - … Journal of Peptide …, 1996 - Wiley Online Library
The 42‐amino acid Aβ, the major constituent of the senile plaque deposits of the brains of
Alzheimer's disease patients, exhibits a high degree of heterogeneity at its N‐terminus …

Structural interconversion in Alzheimer's Amyloid-β (16–35) peptide in an aqueous solution

NA Alves, RB Frigori - The Journal of Physical Chemistry B, 2018 - ACS Publications
Structural properties of Aβ (16–35) fragment are investigated as a model for the amyloid-β
peptide excluding its coil-inducing terminals. Our replica-exchange molecular dynamics …

Promotion and inhibition of amyloid-β peptide aggregation: Molecular dynamics studies

SG Itoh, H Okumura - International Journal of Molecular Sciences, 2021 - mdpi.com
Aggregates of amyloid-β (Aβ) peptides are known to be related to Alzheimer's disease. Their
aggregation is enhanced at hydrophilic–hydrophobic interfaces, such as a cell membrane …

Molecular simulation of the primary and secondary structures of the Aβ (1‐42)‐peptide of Alzheimer's disease

PP Mager - Medicinal research reviews, 1998 - Wiley Online Library
The major protein constituent of the deposits of Alzheimer's disease is the so‐called amyloid
β‐peptide (Aβ) which was derived from proteolysis of a large transmembrane amyloid …