Molecular dynamics simulations combined with nuclear magnetic resonance and/or small-angle X-ray scattering data for characterizing intrinsically disordered protein …

M Chan-Yao-Chong, D Durand… - Journal of Chemical …, 2019 - ACS Publications
The concept of intrinsically disordered proteins (IDPs) has emerged relatively slowly, but
over the past 20 years, it has become an intense research area in structural biology. Indeed …

Insights into Aβ aggregation: A molecular dynamics perspective

JE Shea, B Urbanc - Current topics in medicinal chemistry, 2012 - ingentaconnect.com
This article reviews recent molecular dynamics simulations of the Alzheimer's amyloid-β
protein, the primary component of the amyloid plaques found in the brain of Alzheimer's …

Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer

YS Lin, GR Bowman, KA Beauchamp, VS Pande - Biophysical journal, 2012 - cell.com
The aggregation of amyloid beta (Aβ) peptides plays an important role in the development of
Alzheimer's disease. Despite extensive effort, it has been difficult to characterize the …

Structures of the Amyloid β-Peptides Aβ1–40 and Aβ1–42 as Influenced by pH and a d-Peptide

OO Olubiyi, B Strodel - The Journal of Physical Chemistry B, 2012 - ACS Publications
In this simulation study, we present a comparison of the secondary structure of the two major
alloforms of the Alzheimer's peptide (Aβ1–40 and Aβ1–42) on the basis of molecular …

Self-assembly of α-helical polypeptides into microscopic and enantiomorphic spirals

CD Vacogne, C Wei, K Tauer… - Journal of the American …, 2018 - ACS Publications
Helical structures are ubiquitous in biological materials and often serve a structural purpose.
Bioinspired helical materials can be challenging to synthesize and rarely reach the degree …

Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation

T Zhu, X He, JZH Zhang - Physical Chemistry Chemical Physics, 2012 - pubs.rsc.org
Fragment density functional theory (DFT) calculation of NMR chemical shifts for several
proteins (Trp-cage, Pin1 WW domain, the third IgG-binding domain of Protein G (GB3) and …

Conformational dynamics of the partially disordered yeast transcription factor GCN4

P Robustelli, N Trbovic, RA Friesner… - Journal of chemical …, 2013 - ACS Publications
Molecular dynamics (MD) simulations have been employed to study the conformational
dynamics of the partially disordered DNA binding basic leucine zipper domain of the yeast …

Structure of ring-shaped Aβ42 oligomers determined by conformational selection

L Tran, N Basdevant, C Prévost, T Ha-Duong - Scientific reports, 2016 - nature.com
The oligomerization of amyloid beta (Aβ) peptides into soluble non-fibrillar species plays a
critical role in the pathogenesis of Alzheimer's disease. However, it has been challenging to …

Structure-based experimental datasets for benchmarking of protein simulation force fields

CE Cavender, DA Case, JCH Chen, LT Chong… - arXiv preprint arXiv …, 2023 - arxiv.org
This review article provides an overview of structurally oriented, experimental datasets that
can be used to benchmark protein force fields, focusing on data generated by nuclear …

Structural heterogeneity in familial Alzheimer's disease mutants of amyloid-beta peptides

SH Chong, J Yim, S Ham - Molecular BioSystems, 2013 - pubs.rsc.org
Alzheimer's disease is a neurodegenerative disorder characterized by progressive
deposition of amyloid-beta (Aβ) peptides in brain parenchyma and cerebral blood vessels …