Transformation Between α-Helix and β-Sheet Structures of One and Two Polyglutamine Peptides in Explicit Water Molecules by Replica-Exchange Molecular Dynamics Simulations

Aggregation of polyglutamine peptides with beta-sheet structures is related to some important neurodegenerative diseases such as Huntington's disease. However, it is not clear how polyglutamine peptides form the beta-sheets and aggregate. To understand this problem, we performed all-atom replica-exchange molecular dynamics simulations of one and two polyglutamine peptides with 10 glutamine residues in explicit water molecules. Our results show that two polyglutamine peptides mainly formed helix or coil structures when they are separated, as in the system with one-polyglutamine peptide. As the interpeptide distance decreases, the intrapeptide beta-sheet structure sometimes appear as an intermediate state, and finally the interpeptide beta-sheets are formed. We also find that the polyglutamine dimer tends to form the antiparallel beta-sheet conformations rather than the parallel beta-sheet, which is consistent with previous experiments and a coarse-grained molecular dynamics simulation. (C) 2014 Wiley Periodicals, Inc.