Atomic Level Characterization of PolyGlycine Assembly

Abstract

Polyglycine peptides can adopt polyproline II (PPII) helical conformations that assemble into honeycomb-shaped oligomers. These polyglycine II (PGII) helical bundles, which are also found in several natural proteins, lack apolar groups and cannot be stabilized by hydrophobic interactions. Thus, their folding must differ from that of typical globular proteins for which hydrophobic interactions promote structure formation. Despite their fundamental interest and relevance for molecular pathology, the atomic level details on how these PGII assemblies form are scarcely explored. To elucidate this process, we used CD and NMR spectroscopies to show that oligoglycine peptides with a few terminal Asp residues readily form oligomers rich in PPII helix at low pH and cool temperatures. Next, to test whether these structures can emerge without a preformed template, we performed ten independent, unbiased, multi-microsecond, all-atom molecular dynamics simulations starting from dispersed, terminally capped nonaglycine monomers in water. We observed PPII helical bundle formation through an oligomeric intermediate that is relatively poor in nematic order and H-bonds.