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Simon Mitternacht and Anders Irbäck
Spontaneous β-barrel formation: an all-atom
Monte Carlo study of Aβ(16-22) oligomerization
Proteins 71 207-214 (2008)
Abstract
Using all-atom Monte Carlo (MC) simulations with implicit water
combined with a cluster size analysis, we study the aggregation
of Aβ(16-22), a peptide capable of forming amyloid fibrils.
We consider a system of six initially randomly oriented
Aβ(16-22) 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 β-sheet rich aggregates
at low temperature. At the crossover between these two regimes, we
find that clusters of all sizes occur, whereas the β-strand
content is low. In one of several runs, we observe the spontaneous
formation of a β-barrel with six antiparallel strands. The
β-barrel stands out as the by far most long-lived aggregate
seen in our simulations.
LU TP 07-04
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