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Spontaneous beta-barrel formation: an all-atom study of Abeta(16-22) oligomerization

Irbäck, Anders LU and Mitternacht, Simon LU (2008) In Proteins 71(1). p.207-214
Abstract
Using all-atom Monte Carlo simulations with implicit water, combined with a cluster size analysis, we study the aggregation of A16-22, a peptide capable of forming amyloid fibrils. We consider a system of six initially randomly oriented A16-22 peptides, and investigate the thermodynamics and structural properties of aggregates formed by this system. The system is unaggregated without ordered secondary structure at high temperature, and forms -sheet rich aggregates at low temperature. At the crossover between these two regimes, we find that clusters of all sizes occur, whereas the -strand content is low. In one of several runs, we observe the spontaneous formation of a -barrel with six antiparallel strands. The -barrel stands out as the by... (More)
Using all-atom Monte Carlo simulations with implicit water, combined with a cluster size analysis, we study the aggregation of A16-22, a peptide capable of forming amyloid fibrils. We consider a system of six initially randomly oriented A16-22 peptides, and investigate the thermodynamics and structural properties of aggregates formed by this system. The system is unaggregated without ordered secondary structure at high temperature, and forms -sheet rich aggregates at low temperature. At the crossover between these two regimes, we find that clusters of all sizes occur, whereas the -strand content is low. In one of several runs, we observe the spontaneous formation of a -barrel with six antiparallel strands. The -barrel stands out as the by far most long-lived aggregate seen in our simulations. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
protein aggregation, self-assembly, cluster size analysis, amyloid-, protein misfolding
in
Proteins
volume
71
issue
1
pages
207 - 214
publisher
John Wiley & Sons
external identifiers
  • wos:000254035500020
  • scopus:40549089901
ISSN
0887-3585
DOI
10.1002/prot.21682
language
English
LU publication?
yes
id
e26d54c9-4c11-4ae7-8b75-05be99ce9409 (old id 796135)
date added to LUP
2007-12-28 00:12:54
date last changed
2017-09-17 05:53:04
@article{e26d54c9-4c11-4ae7-8b75-05be99ce9409,
  abstract     = {Using all-atom Monte Carlo simulations with implicit water, combined with a cluster size analysis, we study the aggregation of A16-22, a peptide capable of forming amyloid fibrils. We consider a system of six initially randomly oriented A16-22 peptides, and investigate the thermodynamics and structural properties of aggregates formed by this system. The system is unaggregated without ordered secondary structure at high temperature, and forms -sheet rich aggregates at low temperature. At the crossover between these two regimes, we find that clusters of all sizes occur, whereas the -strand content is low. In one of several runs, we observe the spontaneous formation of a -barrel with six antiparallel strands. The -barrel stands out as the by far most long-lived aggregate seen in our simulations.},
  author       = {Irbäck, Anders and Mitternacht, Simon},
  issn         = {0887-3585},
  keyword      = {protein aggregation,self-assembly,cluster size analysis,amyloid-,protein misfolding},
  language     = {eng},
  number       = {1},
  pages        = {207--214},
  publisher    = {John Wiley & Sons},
  series       = {Proteins},
  title        = {Spontaneous beta-barrel formation: an all-atom study of Abeta(16-22) oligomerization},
  url          = {http://dx.doi.org/10.1002/prot.21682},
  volume       = {71},
  year         = {2008},
}