Works (4)
Updated: July 5th, 2023 15:55
2014 journal article
Impact of sequence on the molecular assembly of short amyloid peptides
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82(7), 1469–1483.
author keywords: short amyloid peptides; protein aggregation; PRIME20; coarse-grained model; discontinuous molecular dynamics
MeSH headings : Amino Acid Sequence; Amyloid / chemistry; Amyloid / metabolism; Amyloid beta-Peptides / chemistry; Amyloid beta-Peptides / metabolism; Molecular Dynamics Simulation; Protein Conformation
TL;DR:
Analysis of the simulation kinetics and energetics reveals why MV GGVV forms fibrils and GGVVIA does not, and why adding I and A to MVGGVVIA reduces fibrillization and enhances amorphous aggregation into oligomeric structures.
(via Semantic Scholar)
open access via europepmc.org (repository)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2011 journal article
Computer simulation study of amyloid fibril formation by palindromic sequences in prion peptides
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79(7), 2132–2145.
author keywords: computer simulation; peptide; aggregation; coarse-grained model
MeSH headings : Amino Acid Sequence; Amyloid / chemistry; Amyloid / metabolism; Animals; Cricetinae; Inverted Repeat Sequences; Kinetics; Mesocricetus; Mice; Molecular Dynamics Simulation; Peptide Fragments / chemistry; Peptide Fragments / metabolism; Prions / chemistry; Prions / metabolism; Temperature
TL;DR:
The degree of order in the fibrillar structure stems in part from the types of kinetic events leading up to its formation, with AGAAAAGA forming less amorphous structures early in the simulation than VAGAAAAGAV and the ability to form fibrils increases as the chain length and the length of the stretch of hydrophobic residues increase.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2011 journal article
Fibrillization Propensity for Short Designed Hexapeptides Predicted by Computer Simulation
JOURNAL OF MOLECULAR BIOLOGY, 416(4), 598–609.
author keywords: fibrils; fibrillization propensity; fibril stability; coarse-grained model; discontinuous molecular dynamics
MeSH headings : Alzheimer Disease / metabolism; Amyloid / chemistry; Humans; Molecular Dynamics Simulation; Oligopeptides / chemistry; Polymerization; Prion Diseases / metabolism; Protein Stability; Temperature
TL;DR:
The results suggest that the fibrillization temperature (temperature above which fibrils cease to form) is a measure of fibril stability and that by rank ordering the fibillization temperatures of various sequences, PRIME20/DMD simulations could be used to ascertain their relative fibrillsization propensities.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2006 article
Computational approaches to fibril structure and formation
AMYLOID, PRIONS, AND OTHER PROTEIN AGGREGATES, PT B, Vol. 412, pp. 338–365.
MeSH headings : Amyloid / chemistry; Computational Biology / methods; Computer Simulation; Humans; Models, Chemical; Models, Molecular; Protein Conformation; Protein Structure, Secondary
TL;DR:
Two computational approaches used to investigate fibril formation and structure are described: intermediate-resolution discontinuous Molecular dynamics simulations and atomistic molecular dynamics simulations, which provide a useful molecular-level picture of fibrils structure and formation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018