| Assembly of normally soluble proteins into ordered aggregates, known as amyloid fibrils, is a cause or associated symptom of numerous human disorders, including Alzheimer's and the prion diseases. Recent experimental studies have offered tantalizing clues regarding the fibril structure, but our understanding of its assembly is still far from complete. The long term goal of our work is to determine the underlying physical forces responsible for the mis-folding and aggregation of proteins. Since the likely toxic species in the various amyloid diseases is believed to occur either on or off the fibrillization pathway, it is of interest to understand the connection between the protein sequence and the structure of the final product, the fibril. The focus here is on short fragments of amyloid proteins; these are believed to be the "Velcro" that holds the fibrillar structures formed by the parent protein together, and can in fact form fibrils themselves.;Accordingly, the aims of this work are to be able to predict and analyze: how variations in the sequence affect the likelihood that a given peptide will form a fibril, the structure of the fully formed fibril of a given sequence, what types of side chains disrupt assembly, and the kinetic events that occur along the fibrillization pathway. The method used is application of discontinuous molecular dynamics simulation to large systems of peptides that are modeled using PRIME20, a new intermediate--resolution protein force field developed in our group to describe the geometry and energetics for all twenty amino acids. Two different classes of peptides are studied: (1) palindromic aliphatic sequences from the Syrian hamster and mouse prion proteins and variations thereof, and (2) short, truncated amyloid and amyloid-like peptides, some of whose fibril crystal structures have been measured.;We simulate the spontaneous assembly of several short prion and prion-like peptides starting from random initial configurations of random coils. We investigate fibril formation and structure of 48 peptides of palindromic prion sequences, AGAAAAGA (SHaPrP 113-120), VAGAAAAGAV (MoPr 111--120), and related variations, GAAAAAAG, (AG)4, A8, GAAAGAAA, A10, V10, GAVAAAAVAG, and VAVAAAAVAV. We observe that as the chain length and the length of the stretch of hydrophobic residues increase, the ability to form fibrils increases. However as the hydrophobicity of the sequence increases, the ability to form well-ordered structures decreases. Thus, long hydrophobic sequences like VAVAAAAVAV and V10, form slightly disordered aggregates that are partially fibrillar and partially amorphous. Subtle changes in sequence result in slightly different fibril structures.;We study the spontaneous assembly of 48-peptide systems containing the short, amyloid peptide fragments and amyloid-like peptides: VEALYL, MVGGVV, SSTSAA, SNQNNF, GGVVIA, and the de novo designed peptides: STVIIE, STAIIE, STVIAE, STVIFE, STVIVE, STVIGE, and STVIEE. Fibril structure and formation kinetics are analyzed. The short amyloid peptide fragments SSTSAA and SNQNNF form fibrils at low temperatures; MVGGVV forms fibrils at intermediate temperatures, and GGVVIA forms beta-sheets. For the de novo designed peptides, at high simulation temperatures, we observed fibrils for STVIIE, STVIFE and did not observe fibrils for STAIIE, STVIGE and STVIEE in agreement with experiments. The sequence STVIVE, formed fibrils in our simulations but fibrils were not observed in vitro suggesting perhaps that PRIME20 is not robust enough to capture subtle difference in amino acid residues like isoleucine and valine. |
