Spontaneous beta-barrel formation: an all-atom Monte Carlo study of Abeta16-22 oligomerization.
Using all-atom Monte Carlo simulations with implicit water, combined with a cluster size analysis, we study the aggregation of Abeta(16) (-22), a peptide capable of forming amyloid fibrils. We consider a system of six initially randomly oriented Abeta(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 beta-sheet rich aggregates at low temperature. At the crossover between these two regimes, we find that clusters of all sizes occur, whereas the beta-strand content is low. In one of several runs, we observe the spontaneous formation of a beta-barrel with six antiparallel strands. The beta-barrel stands out as the by far most long-lived aggregate seen in our simulations.
Irbäck
Anders
A
Computational Biology and Biological Physics Group, Department of Theoretical Physics, Lund University, SE-223 62 Lund, Sweden. anders@thep.lu.se
Mitternacht
Simon
S
D016000:Cluster Analysis; D003080:Cold Temperature; D019281:Dimerization; D008958:Models, Molecular; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D013816:Thermodynamics; D014867:Water
D010455:Peptides; D014867:Water