Journal
PHYSICAL REVIEW E
Volume 80, Issue 4, Pages -Publisher
AMER PHYSICAL SOC
DOI: 10.1103/PhysRevE.80.041927
Keywords
aggregates (materials); aggregation; crystal structure; free energy; molecular biophysics; Monte Carlo methods; proteins; self-assembly
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Funding
- Welch Foundation [A-1628]
- Searle Foundation
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In this paper, we investigated the spontaneous formation of aggregation structures of amyloid-forming peptide (GGVVIA) using a coarse-grained model and Monte Carlo simulations. The effects of concentration and temperature on the formation of different aggregation structures were studied. Three types of aggregation structures, single-layer beta sheet, amorphous beta-sheet aggregate, and fibril-like structures, were observed in our simulations. The fibril-like structures obtained in simulations have a common cross-beta spine structure in which beta sheets twist in a left-handed fashion. The averaged twisting angle of the beta sheet in the fibril-like structures is 12 degrees +/- 2 degrees. Moreover, it was found that the peptides in the same beta sheets prefer to arrange in a parallel way, which is consistent with the corresponding GGVVIA crystalline structure. On the other hand, it was found that there is a rich family of beta-sheet stacking patterns in the fibril-like structures suggesting that the fibril structures are more complex than the corresponding crystalline structure and there exist many local free-energy minima rather than a distinct global minimum.
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