Aggregation of Aβ40/42 chains in the presence of cyclic neuropeptides investigated by molecular dynamics simulations

PLoS Comput Biol. 2021 Mar 12;17(3):e1008771. doi: 10.1371/journal.pcbi.1008771. eCollection 2021 Mar.

Abstract

Alzheimer's disease is associated with the formation of toxic aggregates of amyloid beta (Aβ) peptides. Despite tremendous efforts, our understanding of the molecular mechanisms of aggregation, as well as cofactors that might influence it, remains incomplete. The small cyclic neuropeptide somatostatin-14 (SST14) was recently found to be the most selectively enriched protein in human frontal lobe extracts that binds Aβ42 aggregates. Furthermore, SST14's presence was also found to promote the formation of toxic Aβ42 oligomers in vitro. In order to elucidate how SST14 influences the onset of Aβ oligomerization, we performed all-atom molecular dynamics simulations of model mixtures of Aβ42 or Aβ40 peptides with SST14 molecules and analyzed the structure and dynamics of early-stage aggregates. For comparison we also analyzed the aggregation of Aβ42 in the presence of arginine vasopressin (AVP), a different cyclic neuropeptide. We observed the formation of self-assembled aggregates containing the Aβ chains and small cyclic peptides in all mixtures of Aβ42-SST14, Aβ42-AVP, and Aβ40-SST14. The Aβ42-SST14 mixtures were found to develop compact, dynamically stable, but small aggregates with the highest exposure of hydrophobic residues to the solvent. Differences in the morphology and dynamics of aggregates that comprise SST14 or AVP appear to reflect distinct (1) regions of the Aβ chains they interact with; (2) propensities to engage in hydrogen bonds with Aβ peptides; and (3) solvent exposures of hydrophilic and hydrophobic groups. The presence of SST14 was found to impede aggregation in the Aβ42-SST14 system despite a high hydrophobicity, producing a stronger "sticky surface" effect in the aggregates at the onset of Aβ42-SST14 oligomerization.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alzheimer Disease
  • Amyloid beta-Peptides* / chemistry
  • Amyloid beta-Peptides* / metabolism
  • Computational Biology
  • Humans
  • Molecular Dynamics Simulation*
  • Peptide Fragments* / chemistry
  • Peptide Fragments* / metabolism
  • Protein Aggregation, Pathological
  • Somatostatin* / chemistry
  • Somatostatin* / metabolism

Substances

  • Amyloid beta-Peptides
  • Peptide Fragments
  • amyloid beta-protein (40-42)
  • Somatostatin

Grants and funding

The work was supported by the Alberta Prion Research Institute (APRI), Projects 201600028 (to HW and GSU) and 201700016 (MS). Philanthropic financial support from the Borden Rosiak family is gratefully acknowledged (to GSU). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.