Atomistic insights into the structure of heptapeptide nanofibers

Francesca Peccati, Mariona Sodupe

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Artificial amyloid-like nanofibers formed from short peptides are emerging as new supramolecular structures for catalysis and advanced materials. In this work, we analyze, by means of computational approaches, the preferred atomistic fibrillar architectures that result from the self-assembly of polar NY7, NF7, SY7, SF7, and GY7 peptides into steric zippers formed by two β-sheets (describing an individual steric zipper) and by four β-sheets. For all heptapeptides, except GY7, parallel β-sheet organizations with polar residues packed at the steric zipper appear to be the preferred assemblies for the two β-sheets system due to the formation of a strong network of hydrogen bonds. For GY7, however, an antiparallel organization with glycine at the steric zipper is the most stable one. The preferred architecture is mostly conserved when enlarging our model from two to four β-sheets. The present work shows that the relative stability of different architectures results from a delicate balance between peptide composition, side chain hydrophobicity, and non-covalent interactions at the interface and provides the basis for a rational design of new improved artificial prion-inspired materials.

Original languageEnglish
Article number055101
JournalThe Journal of Chemical Physics
Volume155
Issue number5
DOIs
Publication statusPublished - 7 Aug 2021

Keywords

  • Amyloidogenic Proteins/chemistry
  • Hydrogen Bonding
  • Molecular Dynamics Simulation
  • Nanofibers/chemistry
  • Oligopeptides/chemistry
  • Protein Conformation, beta-Strand
  • Thermodynamics

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