Journal of Physics: Conference Series 627, 012028 (2015)

ISSN: 1742-6596

Aggregation of peptides in the tube model with correlated sidechain orientations

Nguyen Ba Hung and Trinh Xuan Hoang

The ability of proteins and peptides to aggregate and form toxic amyloid fibrils is associated with a range of diseases including BSE (or mad cow), Alzheimer's and Parkinson's Diseases. In this study, we investigate the the role of amino acid sequence in the aggregation propensity by using a modified tube model with a new procedure for hydrophobic interaction. In this model, the amino acid sidechains are not considered explicitly, but their orientations are taken into account in the formation of hydrophobic contact. Extensive Monte Carlo simulations for systems of short peptides are carried out with the use of parallel tempering technique. Our results show that the propensity to form and the structures of the aggregates strongly depend on the amino acid sequence and the number of peptides. Some sequences may not aggregate at all at a presumable physiological temperature while other can easily form fibril-like β-sheet struture. Our study provides an insight into the principles of how the formation of amyloid can be governed by amino acid sequence.

DOI: doi:10.1088/1742-6596/627/1/012028

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