Nanomechanics of functional and pathological amyloid materials

TPJ Knowles, MJ Buehler - Nature nanotechnology, 2011‏ - nature.com
Amyloid or amyloid-like fibrils represent a general class of nanomaterials that can be formed
from many different peptides and proteins. Although these structures have an important role …

Islet amyloid polypeptide: structure, function, and pathophysiology

R Akter, P Cao, H Noor, Z Ridgway… - Journal of diabetes …, 2016‏ - Wiley Online Library
The hormone islet amyloid polypeptide (IAPP, or amylin) plays a role in glucose
homeostasis but aggregates to form islet amyloid in type‐2 diabetes. Islet amyloid formation …

Molecular mechanism of thioflavin-T binding to the surface of β-rich peptide self-assemblies

M Biancalana, K Makabe, A Koide, S Koide - Journal of molecular biology, 2009‏ - Elsevier
A number of small organic molecules have been developed that bind to amyloid fibrils, a
subset of which also inhibit fibrillization. Among these, the benzothiol dye Thioflavin-T (ThT) …

Are current atomistic force fields accurate enough to study proteins in crowded environments?

D Petrov, B Zagrovic - PLoS Computational Biology, 2014‏ - journals.plos.org
The high concentration of macromolecules in the crowded cellular interior influences
different thermodynamic and kinetic properties of proteins, including their structural …

Simulations as analytical tools to understand protein aggregation and predict amyloid conformation

B Ma, R Nussinov - Current opinion in chemical biology, 2006‏ - Elsevier
Computational tools are increasingly being applied to solve the protein aggregation
problem, providing insight into amyloid structures and aggregation mechanisms. The …

Self-assembly of functional, amphipathic amyloid monolayers by the fungal hydrophobin EAS

I Macindoe, AH Kwan, Q Ren, VK Morris… - Proceedings of the …, 2012‏ - pnas.org
The hydrophobin EAS from the fungus Neurospora crassa forms functional amyloid fibrils
called rodlets that facilitate spore formation and dispersal. Self-assembly of EAS into fibrillar …

Modeling the Alzheimer Aβ17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities

J Zheng, H Jang, B Ma, CJ Tsai, R Nussinov - Biophysical journal, 2007‏ - cell.com
We investigate Aβ 17-42 protofibril structures in solution using molecular dynamics
simulations. Recently, NMR and computations modeled the Aβ protofibril as a longitudinal …

Aggregation in protein-based biotherapeutics: computational studies and tools to identify aggregation-prone regions

NJ Agrawal, S Kumar, X Wang, B Helk, SK Singh… - Journal of …, 2011‏ - Elsevier
Because of their large, complex, and conformationally heterogeneous structures,
biotherapeutics are vulnerable to several physicochemical stresses faced during the various …

Solid-state NMR study of amyloid nanocrystals and fibrils formed by the peptide GNNQQNY from yeast prion protein Sup35p

PCA van der Wel, JR Lewandowski… - Journal of the American …, 2007‏ - ACS Publications
Sup35p is a prion protein found in yeast that contains a prion-forming domain characterized
by a repetitive sequence rich in Gln, Asn, Tyr, and Gly amino acid residues. The peptide …

Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35

J Zheng, B Ma, CJ Tsai, R Nussinov - Biophysical journal, 2006‏ - cell.com
A seven amino acid yeast prion sup-35 fragment (GNNQQNY) forms amyloid fibrils. The
availability of its detailed atomic oligomeric structure makes it a good model for studying the …