Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor
Abstract Biological regulation ubiquitously depends on protein allostery, but the regulatory mechanisms are incompletely understood, especially in proteins that undergo ligand-induced allostery with few structural changes. Here we used hydrogen-deuterium exchange with mass spectrometry (HDX/MS) to m...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-03-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-36798-1 |
| _version_ | 1797778786931965952 |
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| author | Anum Glasgow Helen T. Hobbs Zion R. Perry Malcolm L. Wells Susan Marqusee Tanja Kortemme |
| author_facet | Anum Glasgow Helen T. Hobbs Zion R. Perry Malcolm L. Wells Susan Marqusee Tanja Kortemme |
| author_sort | Anum Glasgow |
| collection | DOAJ |
| description | Abstract Biological regulation ubiquitously depends on protein allostery, but the regulatory mechanisms are incompletely understood, especially in proteins that undergo ligand-induced allostery with few structural changes. Here we used hydrogen-deuterium exchange with mass spectrometry (HDX/MS) to map allosteric effects in a paradigm ligand-responsive transcription factor, the lac repressor (LacI), in different functional states (apo, or bound to inducer, anti-inducer, and/or DNA). Although X-ray crystal structures of the LacI core domain in these states are nearly indistinguishable, HDX/MS experiments reveal widespread differences in flexibility. We integrate these results with modeling of protein-ligand-solvent interactions to propose a revised model for allostery in LacI, where ligand binding allosterically shifts the conformational ensemble as a result of distinct changes in the rigidity of secondary structures in the different states. Our model provides a mechanistic basis for the altered function of distal mutations. More generally, our approach provides a platform for characterizing and engineering protein allostery. |
| first_indexed | 2024-03-12T23:22:35Z |
| format | Article |
| id | doaj.art-ba6d9b9249fd459e87239216ecc307ce |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-12T23:22:35Z |
| publishDate | 2023-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-ba6d9b9249fd459e87239216ecc307ce2023-07-16T11:21:45ZengNature PortfolioNature Communications2041-17232023-03-0114111510.1038/s41467-023-36798-1Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressorAnum Glasgow0Helen T. Hobbs1Zion R. Perry2Malcolm L. Wells3Susan Marqusee4Tanja Kortemme5Department of Bioengineering and Therapeutic Sciences, University of CaliforniaDepartment of Chemistry, University of California, BerkeleyDepartment of Molecular Biophysics and Biochemistry, Yale UniversityDepartment of Physics, Columbia UniversityDepartment of Chemistry, University of California, BerkeleyDepartment of Bioengineering and Therapeutic Sciences, University of CaliforniaAbstract Biological regulation ubiquitously depends on protein allostery, but the regulatory mechanisms are incompletely understood, especially in proteins that undergo ligand-induced allostery with few structural changes. Here we used hydrogen-deuterium exchange with mass spectrometry (HDX/MS) to map allosteric effects in a paradigm ligand-responsive transcription factor, the lac repressor (LacI), in different functional states (apo, or bound to inducer, anti-inducer, and/or DNA). Although X-ray crystal structures of the LacI core domain in these states are nearly indistinguishable, HDX/MS experiments reveal widespread differences in flexibility. We integrate these results with modeling of protein-ligand-solvent interactions to propose a revised model for allostery in LacI, where ligand binding allosterically shifts the conformational ensemble as a result of distinct changes in the rigidity of secondary structures in the different states. Our model provides a mechanistic basis for the altered function of distal mutations. More generally, our approach provides a platform for characterizing and engineering protein allostery.https://doi.org/10.1038/s41467-023-36798-1 |
| spellingShingle | Anum Glasgow Helen T. Hobbs Zion R. Perry Malcolm L. Wells Susan Marqusee Tanja Kortemme Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor Nature Communications |
| title | Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor |
| title_full | Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor |
| title_fullStr | Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor |
| title_full_unstemmed | Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor |
| title_short | Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor |
| title_sort | ligand specific changes in conformational flexibility mediate long range allostery in the lac repressor |
| url | https://doi.org/10.1038/s41467-023-36798-1 |
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