Amyloid-like self-assembly of a dodecapeptide sequence from the adenovirus fiber shaft: Perspectives from molecular dynamics simulations

Peptide and protein self-assembly is related to the fundamental problems of protein folding and misfolding and has potential applications in medicine, materials science and nanotechnology. Sequence repeats from self-assembling proteins may provide useful elementary building blocks of peptide-based nanostructures. Sequences from the adenovirus fiber shaft self-assemble into amyloid-like fibrils outside their native context. In earlier simulations we studied the self-assembly of two shaft sequences, the octapeptide NSGAITIG and the hexapeptide GAITIG. Based on these simulations, cysteine residues were substituted at the first two positions of the octapeptide, yielding amyloid fibrils capable of binding to silver, gold and platinum nanoparticles. Here, we study by implicit-solvent replica-exchange simulations the self-assembly of a longer shaft sequence, the dodecapeptide LSFDNSGAITIG. The simulations provide insights on the molecular organization of the corresponding fibers. Individual molecules tend to adopt hairpin-like conformations in the observed intermolecular β-sheets, in line with the experimentally determined amyloid fiber diameters and the conformation of the peptide in the adenovirus fiber shaft. By analyzing the arrangement of individual peptides in the intermolecular sheets, we suggest possible structural models of the corresponding fibers and interpret their stability by energetic calculations.