ArticleCommunications biology2023
Does AlphaFold2 model proteins' intracellular conformations? An experimental test using cross-linking mass spectrometry of endogenous ciliary proteins.
Article in Communications biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 33 citations in OpenAlex.
- Bridging structure and function: artificial intelligence-based modelling of kidney proteins.Nature reviews. Nephrology · 2026Review
- Regulation of AP1 adaptor assembly by the bi-handed chaperone MEA1.Nature communications · 2026Article
- NMR in the Age of Modern Biomedical Research and Drug Discovery.Journal of molecular biology · 2025Review
- AFragmenter: schema-free, tuneable protein domain segmentation for AlphaFold protein structures.Bioinformatics (Oxford, England) · 2025Article
- Strategies for multimodal spatiotemporal profiling of phosphorylation in cilia biology.Journal of cell science · 2025Review
- The CAGE complex: a hollow, megadalton, protein assembly in prokaryotic and eukaryotic microbes.bioRxiv : the preprint server for biology · 2025Article
- Bi-handed assembly chaperones regulate protein complex assembly through an intramolecular handover mechanism.Science advances · 2025Article
- A ternary complex of MIPs in the A-tubule of basal bodies and axonemes depends on RIB22 and the EF-hand domain of RIB72A inMolecular biology of the cell · 2025Article
- An amino acid-resolution interactome for motile cilia identifies the structure and function of ciliopathy protein complexes.Developmental cell · 2025Article
- Mass spectrometry-complemented molecular modeling predicts the interaction interface for a camelid single-domain antibody targeting theComputational and structural biotechnology journal · 2024Article
- Article
- AlphaFold two years on: Validation and impact.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins.Nature chemical biology · 2024Review
- Improving AlphaFold Predicted Contacts for Alpha-Helical Transmembrane Proteins Using Structural Features.International journal of molecular sciences · 2024Article
- Functional implication of the homotrimeric multidomain vacuolar sorting receptor 1 (VSR1) from Arabidopsis thaliana.Scientific reports · 2024Article
- DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction.Nature methods · 2024Article
- Systematic analysis of the relationship between fold-dependent flexibility and artificial intelligence protein structure prediction.PloS one · 2024Article
- Higher-Order Structural Organization of the Mitochondrial Proteome Charted by In Situ Cross-Linking Mass Spectrometry.Molecular & cellular proteomics : MCP · 2023Article
- Improving AlphaFold predicted contacts in alpha-helical transmembrane proteins structures using structural features.Research square · 2023Article
- Native doublet microtubules from Tetrahymena thermophila reveal the importance of outer junction proteins.Nature communications · 2023Article
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Authors and funding
5 authors at 1 institution in 1 country.
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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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.