Does AlphaFold2 model proteins’ intracellular conformations? An experimental test using cross-linking mass spectrometry of endogenous ciliary proteins
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Abstract
A major goal in structural biology is to understand protein assemblies in their biologically relevant states. Here, we investigate whether AlphaFold2 structure predictions match native protein conformations. We chemically cross-linked proteins in situ within intact Tetrahymena thermophila cilia and native ciliary extracts, identifying 1,225 intramolecular cross-links within the 100 best-sampled proteins, providing a benchmark of distance restraints obeyed by proteins in their native assemblies. The corresponding structure predictions were highly concordant, positioning 86.2% of cross-linked residues within Cɑ-to-Cɑ distances of 30 Å, consistent with the cross-linker length. 43% of proteins showed no violations. Most inconsistencies occurred in low-confidence regions or between domains. Overall, AlphaFold2 predictions with lower predicted aligned error corresponded to more correct native structures. However, we observe cases where rigid body domains are oriented incorrectly, as for ciliary protein BBC118, suggesting that combining structure prediction with experimental information will better reveal biologically relevant conformations.
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Several groups reported AF2 models with low PAE (<5 Å) that still deviated from experimental data.
“Several groups have reported cases of AF2 models with low PAE values (< 5 Å) that deviated from experimental data62,63”
From The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins (2024) · cites this paper as [62]
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- Authors
- McCafferty, C. L., Pennington, E. L., Papoulas, O., Taylor, D. W., & Marcotte, E. M.
- Affiliations
- The University of Texas at Austin (US)
- Corresponding author
- McCafferty, Caitlyn L.
- Venue
- Communications Biology
- Published
- 2023-04-15
- Volume
- 6
- Issue
- 1
- Pages
- 421-421
- ISSN
- 2399-3642 (ISSN-L)
- PMC
- PMC10105775
- OpenAlex
- W4365816022
- Cited by
- 35
- References
- 58
- Citations by year
- 2026: 4 · 2025: 7 · 2024: 13 · 2023: 10 · 2022: 1
- FWCI
- 3.02
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Communications Biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (R35GM138348, R35GM122480)
- Welch Foundation (F-1938, F-1515)
- Cancer Prevention and Research Institute of Texas (RR160088)
- U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD085901)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Keywords
- AlphaFold2, protein structure prediction, ciliary proteins, Tetrahymena thermophila, cilia, crosslinking, cross-linking mass spectrometry, distance restraints
- MeSH terms
- Protein Conformation, Proteins, Mass Spectrometry
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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