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Deep Learning-based structure modelling illuminates structure and function in uncharted regions of β-solenoid fold

Shahram Mesdaghi1, Rebecca M Price2, Jillian Madine2

  • 1The University of Liverpool, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, Liverpool L69 7ZB, United Kingdom; Computational Biology Facility, MerseyBio, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.

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Deep learning models identified novel beta-solenoid protein structures, revealing their diverse functions in adhesins, mucins, and functional amyloids across life domains.

Keywords:
AdhesinsAlphafold2AmyloidGreek keyTandem repeatsβ-solenoid

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Area of Science:

  • Structural biology
  • Computational biology
  • Protein science

Background:

  • Repeat proteins are ubiquitous, featuring diverse functions and structural motifs.
  • Beta-solenoids, a class of repeat proteins, possess unique structural characteristics like handedness and twist.
  • Many beta-solenoid proteins, crucial in virulence factors and functional amyloids, lack experimental structures due to modeling and crystallization challenges.

Purpose of the Study:

  • To discover novel beta-solenoid protein structures using deep learning.
  • To identify structural neighbors and infer potential functions of predicted beta-solenoids.
  • To explore the structural diversity and functional implications of beta-solenoid folds.

Main Methods:

  • Application of various deep learning-based structure-modeling techniques.
  • Utilizing structural database searches to find homologous proteins.
  • Relating predicted structures to potential biological functions.

Main Results:

  • Discovery of novel eukaryotic and prokaryotic adhesins with beta-solenoid folds.
  • Identification of exceptionally long, flat beta-solenoid structures potentially forming mucin tandem repeats.
  • Characterization of unprecedentedly small beta-solenoid structures and a novel FapC Greek key beta-solenoid fold.

Conclusions:

  • Deep learning effectively predicts diverse beta-solenoid structures and their functions.
  • Confirms the link between beta-solenoid folds and adhesin functionality.
  • Highlights potential roles in mucin structures and Pseudomonas functional amyloid fibers.