Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter
Abstract Here we used cryo-electron microscopy (cryo-EM), double electron-electron resonance spectroscopy (DEER), and molecular dynamics (MD) simulations, to capture and characterize ATP- and substrate-bound inward-facing (IF) and occluded (OC) conformational states of the heterodimeric ATP binding...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-11-01
|
| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-42937-5 |
| _version_ | 1797630119196491776 |
|---|---|
| author | Qingyu Tang Matt Sinclair Hale S. Hasdemir Richard A. Stein Erkan Karakas Emad Tajkhorshid Hassane S. Mchaourab |
| author_facet | Qingyu Tang Matt Sinclair Hale S. Hasdemir Richard A. Stein Erkan Karakas Emad Tajkhorshid Hassane S. Mchaourab |
| author_sort | Qingyu Tang |
| collection | DOAJ |
| description | Abstract Here we used cryo-electron microscopy (cryo-EM), double electron-electron resonance spectroscopy (DEER), and molecular dynamics (MD) simulations, to capture and characterize ATP- and substrate-bound inward-facing (IF) and occluded (OC) conformational states of the heterodimeric ATP binding cassette (ABC) multidrug exporter BmrCD in lipid nanodiscs. Supported by DEER analysis, the structures reveal that ATP-powered isomerization entails changes in the relative symmetry of the BmrC and BmrD subunits that propagates from the transmembrane domain to the nucleotide binding domain. The structures uncover asymmetric substrate and Mg2+ binding which we hypothesize are required for triggering ATP hydrolysis preferentially in one of the nucleotide-binding sites. MD simulations demonstrate that multiple lipid molecules differentially bind the IF versus the OC conformation thus establishing that lipid interactions modulate BmrCD energy landscape. Our findings are framed in a model that highlights the role of asymmetric conformations in the ATP-coupled transport with general implications to the mechanism of ABC transporters. |
| first_indexed | 2024-03-11T11:03:25Z |
| format | Article |
| id | doaj.art-a047436bdf4c4cb998566188a7b94142 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-11T11:03:25Z |
| publishDate | 2023-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-a047436bdf4c4cb998566188a7b941422023-11-12T12:23:33ZengNature PortfolioNature Communications2041-17232023-11-0114111610.1038/s41467-023-42937-5Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporterQingyu Tang0Matt Sinclair1Hale S. Hasdemir2Richard A. Stein3Erkan Karakas4Emad Tajkhorshid5Hassane S. Mchaourab6Department of Molecular Physiology and Biophysics, Vanderbilt UniversityTheoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignTheoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignDepartment of Molecular Physiology and Biophysics, Vanderbilt UniversityDepartment of Molecular Physiology and Biophysics, Vanderbilt UniversityTheoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignDepartment of Molecular Physiology and Biophysics, Vanderbilt UniversityAbstract Here we used cryo-electron microscopy (cryo-EM), double electron-electron resonance spectroscopy (DEER), and molecular dynamics (MD) simulations, to capture and characterize ATP- and substrate-bound inward-facing (IF) and occluded (OC) conformational states of the heterodimeric ATP binding cassette (ABC) multidrug exporter BmrCD in lipid nanodiscs. Supported by DEER analysis, the structures reveal that ATP-powered isomerization entails changes in the relative symmetry of the BmrC and BmrD subunits that propagates from the transmembrane domain to the nucleotide binding domain. The structures uncover asymmetric substrate and Mg2+ binding which we hypothesize are required for triggering ATP hydrolysis preferentially in one of the nucleotide-binding sites. MD simulations demonstrate that multiple lipid molecules differentially bind the IF versus the OC conformation thus establishing that lipid interactions modulate BmrCD energy landscape. Our findings are framed in a model that highlights the role of asymmetric conformations in the ATP-coupled transport with general implications to the mechanism of ABC transporters.https://doi.org/10.1038/s41467-023-42937-5 |
| spellingShingle | Qingyu Tang Matt Sinclair Hale S. Hasdemir Richard A. Stein Erkan Karakas Emad Tajkhorshid Hassane S. Mchaourab Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter Nature Communications |
| title | Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter |
| title_full | Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter |
| title_fullStr | Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter |
| title_full_unstemmed | Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter |
| title_short | Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter |
| title_sort | asymmetric conformations and lipid interactions shape the atp coupled cycle of a heterodimeric abc transporter |
| url | https://doi.org/10.1038/s41467-023-42937-5 |
| work_keys_str_mv | AT qingyutang asymmetricconformationsandlipidinteractionsshapetheatpcoupledcycleofaheterodimericabctransporter AT mattsinclair asymmetricconformationsandlipidinteractionsshapetheatpcoupledcycleofaheterodimericabctransporter AT haleshasdemir asymmetricconformationsandlipidinteractionsshapetheatpcoupledcycleofaheterodimericabctransporter AT richardastein asymmetricconformationsandlipidinteractionsshapetheatpcoupledcycleofaheterodimericabctransporter AT erkankarakas asymmetricconformationsandlipidinteractionsshapetheatpcoupledcycleofaheterodimericabctransporter AT emadtajkhorshid asymmetricconformationsandlipidinteractionsshapetheatpcoupledcycleofaheterodimericabctransporter AT hassanesmchaourab asymmetricconformationsandlipidinteractionsshapetheatpcoupledcycleofaheterodimericabctransporter |