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