What can AlphaFold do for antimicrobial amyloids?

Peleg Ragonis-Bachar, Gabriel Axel, Shahar Blau, Nir Ben-Tal, Rachel Kolodny, Meytal Landau

Research output: Contribution to journalArticlepeer-review

Abstract

Amyloids, protein, and peptide assemblies in various organisms are crucial in physiological and pathological processes. Their intricate structures, however, present significant challenges, limiting our understanding of their functions, regulatory mechanisms, and potential applications in biomedicine and technology. This study evaluated the AlphaFold2 ColabFold method's structure predictions for antimicrobial amyloids, using eight antimicrobial peptides (AMPs), including those with experimentally determined structures and AMPs known for their distinct amyloidogenic morphological features. Additionally, two well-known human amyloids, amyloid-β and islet amyloid polypeptide, were included in the analysis due to their disease relevance, short sequences, and antimicrobial properties. Amyloids typically exhibit tightly mated β-strand sheets forming a cross-β configuration. However, certain amphipathic α-helical subunits can also form amyloid fibrils adopting a cross-α structure. Some AMPs in the study exhibited a combination of cross-α and cross-β amyloid fibrils, adding complexity to structure prediction. The results showed that the AlphaFold2 ColabFold models favored α-helical structures in the tested amyloids, successfully predicting the presence of α-helical mated sheets and a hydrophobic core resembling the cross-α configuration. This implies that the AI-based algorithms prefer assemblies of the monomeric state, which was frequently predicted as helical, or capture an α-helical membrane-active form of toxic peptides, which is triggered upon interaction with lipid membranes.

Original languageEnglish
Pages (from-to)265-281
Number of pages17
JournalProteins: Structure, Function and Bioinformatics
Volume92
Issue number2
DOIs
StatePublished - Feb 2024

Bibliographical note

Publisher Copyright:
© 2023 The Authors. Proteins: Structure, Function, and Bioinformatics published by Wiley Periodicals LLC.

Keywords

  • AlphaFold
  • amyloids
  • antimicrobial peptides
  • cross-alpha
  • cross-beta

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology
  • Biochemistry

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