Does AlphaFold2 model proteins’ intracellular conformations? An experimental test using cross-linking mass spectrometry of endogenous ciliary proteins
Year: 2023
Type: article
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.
Source: Communications Biology
Institution: The University of Texas at Austin
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,690
Funders: National Science Foundation, U.S. Department of Health and Human Services, Welch Foundation, Cancer Prevention and Research Institute of Texas, University of Texas at Austin, DeepMind, National Institute of General Medical Sciences, National Institute of Child Health and Human Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development
Awards: G1056835623, G1208658276, G1346015802, G1886213718, G2932541595, G36876509, G3899806454, G4682064022, G551418462, G5610185537, G57775982, G6231699077, G6639017072, Imaging macromolecular machines in gene regulation, Recruitment of First-Time, Tenure-Track Faculty Members, G751837297, G764849402, Proteomics and model organism humanization to decode human genetics, Mapping the ciliary interactome, an extensive protein interaction network underlying human ciliopathies
OpenAlex ID: W4365816022