Computational methods in nanostructure design: Replica exchange simulations of self-assembling peptides

Abstract

Self-assembling peptides can serve as building blocks for novel biomaterials. Replica exchange molecular dynamics simulations are a powerful means to probe the conformational space of these peptides. We discuss the theoretical foundations of this enhanced sampling method and its use in biomolecular simulations. We then apply this method to determine the monomeric conformations of the Alzheimer amyloid-β(12-28) peptide that can serve as initiation sites for aggregation. © 2008 Humana Press.