3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase
Abstract Advances in X-ray crystallography and cryogenic electron microscopy (cryo-EM) offer the promise of elucidating functionally relevant conformational changes that are not easily studied by other biophysical methods. Here we show that 3D variability analysis (3DVA) of the cryo-EM map for wild-...
Saved in:
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2024-12-01
|
| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-54912-9 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849220633836126208 |
|---|---|
| author | Adriana Coricello Alanya J. Nardone Antonio Lupia Carmen Gratteri Matthijn Vos Vincent Chaptal Stefano Alcaro Wen Zhu Yuichiro Takagi Nigel G. J. Richards |
| author_facet | Adriana Coricello Alanya J. Nardone Antonio Lupia Carmen Gratteri Matthijn Vos Vincent Chaptal Stefano Alcaro Wen Zhu Yuichiro Takagi Nigel G. J. Richards |
| author_sort | Adriana Coricello |
| collection | DOAJ |
| description | Abstract Advances in X-ray crystallography and cryogenic electron microscopy (cryo-EM) offer the promise of elucidating functionally relevant conformational changes that are not easily studied by other biophysical methods. Here we show that 3D variability analysis (3DVA) of the cryo-EM map for wild-type (WT) human asparagine synthetase (ASNS) identifies a functional role for the Arg-142 side chain and test this hypothesis experimentally by characterizing the R142I variant in which Arg-142 is replaced by isoleucine. Support for Arg-142 playing a role in the intramolecular translocation of ammonia between the active site of the enzyme is provided by the glutamine-dependent synthetase activity of the R142 variant relative to WT ASNS, and MD simulations provide a possible molecular mechanism for these findings. Combining 3DVA with MD simulations is a generally applicable approach to generate testable hypotheses of how conformational changes in buried side chains might regulate function in enzymes. |
| format | Article |
| id | doaj-art-22f449e680ca4a2fa2a7745c2d6980bc |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-22f449e680ca4a2fa2a7745c2d6980bc2024-12-08T12:37:05ZengNature PortfolioNature Communications2041-17232024-12-0115111510.1038/s41467-024-54912-93D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetaseAdriana Coricello0Alanya J. Nardone1Antonio Lupia2Carmen Gratteri3Matthijn Vos4Vincent Chaptal5Stefano Alcaro6Wen Zhu7Yuichiro Takagi8Nigel G. J. Richards9Dipartimento di Scienze della Salute, Università “Magna Græcia” di CatanzaroDepartment of Chemistry & Biochemistry, Florida State UniversityNet4Science Academic Spin-Off, Università “Magna Græcia” di CatanzaroDipartimento di Scienze della Salute, Università “Magna Græcia” di CatanzaroNanoImaging Core Facility, Centre de Resources et Recherches Technologiques, Institut PasteurMolecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of LyonDipartimento di Scienze della Salute, Università “Magna Græcia” di CatanzaroDepartment of Chemistry & Biochemistry, Florida State UniversityDepartment of Biochemistry & Molecular Biology, Indiana University School of MedicineSchool of Chemistry, Cardiff UniversityAbstract Advances in X-ray crystallography and cryogenic electron microscopy (cryo-EM) offer the promise of elucidating functionally relevant conformational changes that are not easily studied by other biophysical methods. Here we show that 3D variability analysis (3DVA) of the cryo-EM map for wild-type (WT) human asparagine synthetase (ASNS) identifies a functional role for the Arg-142 side chain and test this hypothesis experimentally by characterizing the R142I variant in which Arg-142 is replaced by isoleucine. Support for Arg-142 playing a role in the intramolecular translocation of ammonia between the active site of the enzyme is provided by the glutamine-dependent synthetase activity of the R142 variant relative to WT ASNS, and MD simulations provide a possible molecular mechanism for these findings. Combining 3DVA with MD simulations is a generally applicable approach to generate testable hypotheses of how conformational changes in buried side chains might regulate function in enzymes.https://doi.org/10.1038/s41467-024-54912-9 |
| spellingShingle | Adriana Coricello Alanya J. Nardone Antonio Lupia Carmen Gratteri Matthijn Vos Vincent Chaptal Stefano Alcaro Wen Zhu Yuichiro Takagi Nigel G. J. Richards 3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase Nature Communications |
| title | 3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase |
| title_full | 3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase |
| title_fullStr | 3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase |
| title_full_unstemmed | 3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase |
| title_short | 3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase |
| title_sort | 3d variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase |
| url | https://doi.org/10.1038/s41467-024-54912-9 |
| work_keys_str_mv | AT adrianacoricello 3dvariabilityanalysisrevealsahiddenconformationalchangecontrollingammoniatransportinhumanasparaginesynthetase AT alanyajnardone 3dvariabilityanalysisrevealsahiddenconformationalchangecontrollingammoniatransportinhumanasparaginesynthetase AT antoniolupia 3dvariabilityanalysisrevealsahiddenconformationalchangecontrollingammoniatransportinhumanasparaginesynthetase AT carmengratteri 3dvariabilityanalysisrevealsahiddenconformationalchangecontrollingammoniatransportinhumanasparaginesynthetase AT matthijnvos 3dvariabilityanalysisrevealsahiddenconformationalchangecontrollingammoniatransportinhumanasparaginesynthetase AT vincentchaptal 3dvariabilityanalysisrevealsahiddenconformationalchangecontrollingammoniatransportinhumanasparaginesynthetase AT stefanoalcaro 3dvariabilityanalysisrevealsahiddenconformationalchangecontrollingammoniatransportinhumanasparaginesynthetase AT wenzhu 3dvariabilityanalysisrevealsahiddenconformationalchangecontrollingammoniatransportinhumanasparaginesynthetase AT yuichirotakagi 3dvariabilityanalysisrevealsahiddenconformationalchangecontrollingammoniatransportinhumanasparaginesynthetase AT nigelgjrichards 3dvariabilityanalysisrevealsahiddenconformationalchangecontrollingammoniatransportinhumanasparaginesynthetase |