Amyloid β protein and Alzheimer's disease: When computer simulations complement experimental studies

J Nasica-Labouze, PH Nguyen, F Sterpone… - Chemical …, 2015 - ACS Publications
Alzheimer's disease (AD) challenges our society with an annual estimated cost of $1.08
trillion in the United States alone by 2050. 1 AD is a progressive irreversible neurological …

Simulation studies of amyloidogenic polypeptides and their aggregates

IM Ilie, A Caflisch - Chemical reviews, 2019 - ACS Publications
Amyloids, fibrillar assembly of (poly) peptide chains, are associated with neurodegenerative
illnesses such as Alzheimer's and Parkinson's diseases, for which there are no cures. The …

Biochemistry of amyloid β-protein and amyloid deposits in Alzheimer disease

CL Masters, DJ Selkoe - Cold Spring …, 2012 - perspectivesinmedicine.cshlp.org
Progressive cerebral deposition of the amyloid β-protein (Aβ) in brain regions serving
memory and cognition is an invariant and defining feature of Alzheimer disease. A highly …

Structures of the intrinsically disordered Aβ, tau and α-synuclein proteins in aqueous solution from computer simulations

PH Nguyen, P Derreumaux - Biophysical Chemistry, 2020 - Elsevier
Intrinsically disordered proteins (IDPs) play many biological roles in the human proteome
ranging from vesicular transport, signal transduction to neurodegenerative diseases. The Aβ …

Polymorphism in Alzheimer Aβ amyloid organization reflects conformational selection in a rugged energy landscape

Y Miller, B Ma, R Nussinov - Chemical reviews, 2010 - ACS Publications
Amyloids can have normal biological functions. 1r3 However, amyloidogenic proteins can
also form unwanted oligomeric or polymeric aggregates when disturbed from their native …

Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of Aβ16–22 Dimer

VH Man, X He, P Derreumaux, B Ji… - Journal of chemical …, 2019 - ACS Publications
We investigated the effects of 17 widely used atomistic molecular mechanics force fields
(MMFFs) on the structures and kinetics of amyloid peptide assembly. To this end, we …

High-resolution structures of the amyloid-β 1–42 dimers from the comparison of four atomistic force fields

VH Man, PH Nguyen… - The Journal of Physical …, 2017 - ACS Publications
The dimer of the amyloid-β peptide Aβ of 42 residues is the smallest toxic species in
Alzheimer's disease, but its equilibrium structures are unknown. Here we determined the …

Comparison of force fields for Alzheimer's A: A case study for intrinsically disordered proteins

M Carballo‐Pacheco, B Strodel - Protein science, 2017 - Wiley Online Library
Intrinsically disordered proteins are essential for biological processes such as cell
signalling, but are also associated to devastating diseases including Alzheimer's disease …

The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems

F Sterpone, S Melchionna, P Tuffery… - Chemical Society …, 2014 - pubs.rsc.org
The OPEP coarse-grained protein model has been applied to a wide range of applications
since its first release 15 years ago. The model, which combines energetic and structural …

[HTML][HTML] The role of water in the primary nucleation of protein amyloid aggregation

JD Camino, P Gracia, N Cremades - Biophysical Chemistry, 2021 - Elsevier
The understanding of the complex conformational landscape of amyloid aggregation and its
modulation by relevant physicochemical and cellular factors is a prerequisite for elucidating …