Does AlphaFold2 model proteins’ intracellular conformations? An experimental test using cross-linking mass spectrometry of endogenous ciliary proteins
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 c...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-04-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-023-04773-7 |
| _version_ | 1797845808620503040 |
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| author | Caitlyn L. McCafferty Erin L. Pennington Ophelia Papoulas David W. Taylor Edward M. Marcotte |
| author_facet | Caitlyn L. McCafferty Erin L. Pennington Ophelia Papoulas David W. Taylor Edward M. Marcotte |
| author_sort | Caitlyn L. McCafferty |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-09T17:44:56Z |
| format | Article |
| id | doaj.art-52df4cef827346098d028bcb11deb9a7 |
| institution | Directory Open Access Journal |
| issn | 2399-3642 |
| language | English |
| last_indexed | 2024-04-09T17:44:56Z |
| publishDate | 2023-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj.art-52df4cef827346098d028bcb11deb9a72023-04-16T11:22:27ZengNature PortfolioCommunications Biology2399-36422023-04-016111010.1038/s42003-023-04773-7Does AlphaFold2 model proteins’ intracellular conformations? An experimental test using cross-linking mass spectrometry of endogenous ciliary proteinsCaitlyn L. McCafferty0Erin L. Pennington1Ophelia Papoulas2David W. Taylor3Edward M. Marcotte4Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of TexasDepartment of Molecular Biosciences, Center for Systems and Synthetic Biology, University of TexasDepartment of Molecular Biosciences, Center for Systems and Synthetic Biology, University of TexasDepartment of Molecular Biosciences, Center for Systems and Synthetic Biology, University of TexasDepartment of Molecular Biosciences, Center for Systems and Synthetic Biology, University of TexasAbstract 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.https://doi.org/10.1038/s42003-023-04773-7 |
| spellingShingle | Caitlyn L. McCafferty Erin L. Pennington Ophelia Papoulas David W. Taylor Edward M. Marcotte Does AlphaFold2 model proteins’ intracellular conformations? An experimental test using cross-linking mass spectrometry of endogenous ciliary proteins Communications Biology |
| title | Does AlphaFold2 model proteins’ intracellular conformations? An experimental test using cross-linking mass spectrometry of endogenous ciliary proteins |
| title_full | Does AlphaFold2 model proteins’ intracellular conformations? An experimental test using cross-linking mass spectrometry of endogenous ciliary proteins |
| title_fullStr | Does AlphaFold2 model proteins’ intracellular conformations? An experimental test using cross-linking mass spectrometry of endogenous ciliary proteins |
| title_full_unstemmed | Does AlphaFold2 model proteins’ intracellular conformations? An experimental test using cross-linking mass spectrometry of endogenous ciliary proteins |
| title_short | Does AlphaFold2 model proteins’ intracellular conformations? An experimental test using cross-linking mass spectrometry of endogenous ciliary proteins |
| title_sort | does alphafold2 model proteins intracellular conformations an experimental test using cross linking mass spectrometry of endogenous ciliary proteins |
| url | https://doi.org/10.1038/s42003-023-04773-7 |
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