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 …

Molecular dynamics study of amyloid formation of two Abl‐SH3 domain peptides

I Liepina, S Ventura, C Czaplewski… - Journal of Peptide …, 2006 - Wiley Online Library
Molecular dynamics (MD) simulations were carried out for two‐strand and ten‐strand β‐
sheets constructed from two peptides corresponding to the diverging turn of two homologous …

Molecular insights into the oligomerization dynamics and conformations of amyloidogenic and non-amyloidogenic amylin from discrete molecular dynamics …

Y Wang, Y Liu, Y Zhang, G Wei, F Ding… - Physical Chemistry …, 2022 - pubs.rsc.org
The amyloid aggregation of human islet amyloid polypeptide (hIAPP) is associated with
pancreatic β-cell death in type 2 diabetes. The S20G substitution of hIAPP (hIAPP (S20G)) …

Molecular dynamics simulations of alanine rich β‐sheet oligomers: Insight into amyloid formation

B Ma, R Nussinov - Protein Science, 2002 - Wiley Online Library
The aggregation observed in protein conformational diseases is the outcome of significant
new β‐sheet structure not present in the native state. Peptide model systems have been …

Determination of the Most Stable Packing of Peptides from Ribosomal S1 Protein, Protein Bgl2p, and Aβ Peptide in β-Layers During Molecular Dynamics Simulations

AV Glyakina, NK Balabaev, OV Galzitskaya - Computer Simulations of …, 2022 - Springer
Our task was to determine the most stable packing of peptides in β-layers to construct an
oligomer structure for fibril growth. The β-layers consisting of eight short peptides with the …

[HTML][HTML] Unfolding of the amyloid β-peptide central helix: mechanistic insights from molecular dynamics simulations

M Ito, J Johansson, R Strömberg, L Nilsson - PloS one, 2011 - journals.plos.org
Alzheimer's disease (AD) pathogenesis is associated with formation of amyloid fibrils
caused by polymerization of the amyloid β-peptide (Aβ), which is a process that requires …

Conformational distribution and α-helix to β-sheet transition of human amylin fragment dimer

R Qi, Y Luo, B Ma, R Nussinov, G Wei - Biomacromolecules, 2014 - ACS Publications
Experiments suggested that the fibrillation of the 11–25 fragment (hIAPP (11–25)) of human
islet amyloid polypeptide (hIAPP or amylin) involves the formation of transient α-helical …

Effect of familial mutations on the interconversion of α-Helix to β-sheet structures in an amyloid-forming peptide: insight from umbrella sampling simulations

SK Mudedla, NA Murugan, H Ågren - ACS Chemical …, 2018 - ACS Publications
Understanding the initial events of aggregation of amyloid β monomers to form β-sheet rich
fibrils is useful for the development of therapeutics for Alzheimer's disease. In this context …

Molecular‐Dynamics Simulations for Amyloid β1–42 Monomer with D‐Aspartic Acid Residues Using Continuous Solvent

A Oda, K Kobayashi, O Takahashi - Chemistry & Biodiversity, 2010 - Wiley Online Library
Molecular‐dynamics simulations of amyloid‐β1–42 peptides including d‐aspartic acid
residues were performed, and their three‐dimensional structures were compared. The …

[PDF][PDF] Role of β-hairpin formation in aggregation: the self-assembly of the amyloid-β (25–35) peptide

L Larini, JE Shea - Biophysical journal, 2012 - cell.com
Abstract The amyloid-β (25–35) peptide plays a key role in the etiology of Alzheimer's
disease due to its extreme toxicity even in the absence of aging. Because of its high …