Rational design of 19F NMR labelling sites to probe protein structure and interactions
Abstract Proteins are investigated in increasingly more complex biological systems, where 19F NMR is proving highly advantageous due to its high gyromagnetic ratio and background-free spectra. Its application has, however, been hindered by limited chemical shift dispersions and an incomprehensive re...
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| Format: | Article |
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Nature Portfolio
2025-05-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-59105-6 |
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| author | Julian O. Streit Sammy H. S. Chan Saifu Daya John Christodoulou |
| author_facet | Julian O. Streit Sammy H. S. Chan Saifu Daya John Christodoulou |
| author_sort | Julian O. Streit |
| collection | DOAJ |
| description | Abstract Proteins are investigated in increasingly more complex biological systems, where 19F NMR is proving highly advantageous due to its high gyromagnetic ratio and background-free spectra. Its application has, however, been hindered by limited chemical shift dispersions and an incomprehensive relationship between chemical shifts and protein structure. Here, we exploit the sensitivity of 19F chemical shifts to ring currents by designing labels with direct contact to a native or engineered aromatic ring. Fifty protein variants predicted by AlphaFold and molecular dynamics simulations show 80–90% success rates and direct correlations of their experimental chemical shifts with the magnitude of the engineered ring current. Our method consequently improves the chemical shift dispersion and through simple 1D experiments enables structural analyses of alternative conformational states, including ribosome-bound folding intermediates, and in-cell measurements of protein-protein interactions and thermodynamics. Our strategy thus provides a simple and sensitive tool to extract residue contact restraints from chemical shifts for previously intractable systems. |
| format | Article |
| id | doaj-art-201483509aee435ba7ccfa3f9cd12da7 |
| institution | DOAJ |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-201483509aee435ba7ccfa3f9cd12da72025-08-20T03:09:20ZengNature PortfolioNature Communications2041-17232025-05-0116111510.1038/s41467-025-59105-6Rational design of 19F NMR labelling sites to probe protein structure and interactionsJulian O. Streit0Sammy H. S. Chan1Saifu Daya2John Christodoulou3Institute of Structural and Molecular Biology, University College London and Birkbeck CollegeInstitute of Structural and Molecular Biology, University College London and Birkbeck CollegeInstitute of Structural and Molecular Biology, University College London and Birkbeck CollegeInstitute of Structural and Molecular Biology, University College London and Birkbeck CollegeAbstract Proteins are investigated in increasingly more complex biological systems, where 19F NMR is proving highly advantageous due to its high gyromagnetic ratio and background-free spectra. Its application has, however, been hindered by limited chemical shift dispersions and an incomprehensive relationship between chemical shifts and protein structure. Here, we exploit the sensitivity of 19F chemical shifts to ring currents by designing labels with direct contact to a native or engineered aromatic ring. Fifty protein variants predicted by AlphaFold and molecular dynamics simulations show 80–90% success rates and direct correlations of their experimental chemical shifts with the magnitude of the engineered ring current. Our method consequently improves the chemical shift dispersion and through simple 1D experiments enables structural analyses of alternative conformational states, including ribosome-bound folding intermediates, and in-cell measurements of protein-protein interactions and thermodynamics. Our strategy thus provides a simple and sensitive tool to extract residue contact restraints from chemical shifts for previously intractable systems.https://doi.org/10.1038/s41467-025-59105-6 |
| spellingShingle | Julian O. Streit Sammy H. S. Chan Saifu Daya John Christodoulou Rational design of 19F NMR labelling sites to probe protein structure and interactions Nature Communications |
| title | Rational design of 19F NMR labelling sites to probe protein structure and interactions |
| title_full | Rational design of 19F NMR labelling sites to probe protein structure and interactions |
| title_fullStr | Rational design of 19F NMR labelling sites to probe protein structure and interactions |
| title_full_unstemmed | Rational design of 19F NMR labelling sites to probe protein structure and interactions |
| title_short | Rational design of 19F NMR labelling sites to probe protein structure and interactions |
| title_sort | rational design of 19f nmr labelling sites to probe protein structure and interactions |
| url | https://doi.org/10.1038/s41467-025-59105-6 |
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