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