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PreprintCited by 5Protein Structure and DynamicsEnzyme Structure and FunctionAdvanced Electron Microscopy Techniques and Applications

The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.

Exploring the Potential of AlphaFold Distograms for Predicting Binding-induced Hinge Motions

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Savaş, Büşra, Barlas, Ayşe Berçin, Karaca, Ezgi·2025·FEBS Letters
DOI 10.1101/2025.07.25.666757

Preprint — published as 10.1002/1873-3468.70297

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Abstract

AlphaFold models provide static structural predictions, limiting their use in interpreting flexible regions in low-resolution cryo-EM maps. Here, we assess whether AlphaFold-generated distograms can instead reveal conformational flexibility, focusing on binding-induced hinge motions. For this, we examined the key metabolic AK2/AIFM1 complex, where molecular dynamics and cryo-EM confirm a hinge motion in AK2 upon binding. Notably, this motion is captured in the AlphaFold2/3 distograms of apo AK2, even though it is absent in the predicted structures. By extending our analysis to other systems, we demonstrate that distograms may offer a valuable, model-independent method for interpreting ambiguous regions in cryo-EM maps.

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Metadata

Authors
Savaş, B., Barlas, A. B., & Karaca, E.
Affiliations
Dokuz Eylül University (TR)
Corresponding author
Karaca, Ezgi
ORCID
Venue
FEBS Letters
Publisher
openRxiv
Published
2025-07-27
Volume
600
Issue
10
Pages
1558-1570
ISSN
0014-5793 (ISSN-L)
DOI
10.1101/2025.07.25.666757
OpenAlex
W7127579793
Cited by
5
References
3
Citations by year
2026: 3 · 2025: 2
FWCI
6.16
Type
journal article
Language
en
Open access
Licence
creativecommons.org/licenses/by-nc/4.0/ (vor)
Locations
  • FEBS Letters (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
Funders
EMBO (Installation Grant 4421)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
Keywords
hinge motion, conformational flexibility, protein-protein binding, apo structure, protein structure prediction
MeSH terms
Models, Molecular, Motion, Protein Binding, Protein Conformation, Cryoelectron Microscopy, Molecular Dynamics Simulation

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