Cited by 88Protein Structure and DynamicsAlzheimer's disease research and treatmentsPrion Diseases and Protein Misfolding

AlphaFold and the amyloid landscape

Pinheiro, Francisca, Santos, Jaime, Ventura, Salvador·2021·Journal of Molecular Biology

Abstract

Protein aggregation is a widespread phenomenon with important implications in many scientific areas. Although amyloid formation is typically considered as detrimental, functional amyloids that perform physiological roles have been identified in all kingdoms of life. Despite their functional and pathological relevance, the structural details of the majority of molecular species involved in the amyloidogenic process remains elusive. Here, we explore the application of AlphaFold, a highly accurate protein structure predictor, in the field of protein aggregation. While we envision a straightforward application of AlphaFold in assisting the design of globular proteins with improved solubility for biomedical and industrial purposes, the use of this algorithm for predicting the structure of aggregated species seems far from trivial. First, in amyloid diseases, the presence of multiple amyloid polymorphs and the heterogeneity of aggregation intermediates challenges the "one sequence, one structure" paradigm, inherent to sequence-based predictions. Second, aberrant aggregation is not the subject of positive selective pressure, precluding the use of evolutionary-based approaches, which are the core of the AlphaFold pipeline. Instead, amyloid polymorphism seems to be constrained by the need for a defined structure-activity relationship in functional amyloids. They may thus provide a starting point for the application of AlphaFold in the amyloid landscape.

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Crossref · 10.1016/j.jmb.2021.167059

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Authors
Pinheiro, F., Santos, J., & Ventura, S.
Affiliations
Universitat Autònoma de Barcelona (ES)
Corresponding author
  • Pinheiro, Francisca
  • Ventura, Salvador
Venue
Journal of Molecular Biology
Publisher
Elsevier BV
Published
2021-10
Volume
433
Issue
20
Pages
167059
ISSN
0022-2836 (ISSN-L)
OpenAlex
W3165398695
Cited by
88
References
164
Citations by year
2026: 7 · 2025: 13 · 2024: 16 · 2023: 30 · 2022: 15 · 2021: 7
FWCI
1.78
Type
journal article
Language
en
Open access
closed
Locations
  • Journal of Molecular Biology (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • Universitat Autònoma de Barcelona (FPU17/01157)
  • Institució Catalana de Recerca i Estudis Avançats
  • Ministerio de Ciencia e Innovación (PID2019-105017RB-I00)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Prion Diseases and Protein Misfolding
Keywords
AlphaFold, protein aggregation, amyloid polymorphism, functional amyloids, amyloidosis, aggregation intermediates, protein structure prediction, structure-activity relationship
MeSH terms
Amyloid, Amyloidosis, Animals, Humans, Models, Molecular, Protein Conformation, Software, Protein Folding, Protein Aggregation, Pathological, Protein Aggregates

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