title: Aggregation of small peptides studied by molecular dynamics simulations.
abstract: Peptides and proteins tend to aggregate under appropriate conditions. The amyloid fibrils that are ubiquitously found among these structures are associated with major human diseases like Alzheimer's disease, type II diabetes, and various prion diseases. Lately, it has been observed that even very short peptides like tetra and pentapeptides can form ordered amyloid structures. Here, we present aggregation studies of three such small polypeptide systems, namely, the two amyloidogenic peptides DFNKF and FF, and a control (nonamyloidogenic) one, the AGAIL. The respective aggregation process is studied by all-atom Molecular Dynamics simulations, which allow to shed light on the fine details of the association and aggregation process. Our analysis suggests that naturally aggregating systems exhibit significantly diverse overall cluster shape properties and specific intermolecular interactions. Additional analysis was also performed on the previously studied NFGAIL system.
authors.affiliation: Department of Chemistry, University of Rome La Sapienza, Rome 00185, Italy. floeck@caspur.it
authors.forename: Dagmar
authors.initials: D
authors.lastname: Flöck
authors.forename: Giulia
authors.initials: G
authors.lastname: Rossetti
authors.forename: Isabella
authors.initials: I
authors.lastname: Daidone
authors.forename: Andrea
authors.initials: A
authors.lastname: Amadei
authors.forename: Alfredo
authors.initials: A
authors.lastname: Di Nola
mesh_terms: D003198:Computer Simulation; D019281:Dimerization; D006801:Humans; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation
chemical_list: D010455:Peptides